Statistics Summary Report for SPINE Center | Last updated: Aug 21 2008 |
Target Status Statistics
Total number of targets deposited by SPINE to TargetDB: 1095 View SPINE Target List
Table 1: Status Statistics for SPINE
| Status | Total Number of Targets | (%) Relative to "Cloned" Targets | (%) Relative to "Expressed" Targets | (%) Relative to "Purified" Targets | (%) Relative to "Crystallized" Targets |
| Cloned | 633 | 100.0 | - | - | - |
| Expressed | 474 | 74.9 | 100.0 | - | - |
| Soluble | 309 | 48.8 | 65.2 | - | - |
| Purified | 197 | 31.1 | 41.6 | 100.0 | - |
| Crystallized | 72 | 11.4 | 15.2 | 36.5 | 100.0 |
| Diffraction-quality Crystals | 52 | 8.2 | 11.0 | 26.4 | 72.2 |
| Diffraction | 40 | 6.3 | 8.4 | 20.3 | 55.6 |
| NMR Assigned | 29 | 4.6 | 6.1 | 14.7 | - |
| HSQC | 49 | 7.7 | 10.3 | 24.9 | - |
| Crystal Structure | 74 | 11.7 | 15.6 | 37.6 | 102.8 |
| NMR Structure | 28 | 4.4 | 5.9 | 14.2 | - |
| In PDB1 | 67 | 10.6 | 14.1 | 34.0 | 57 |
| Work Stopped | 3 | - | - | - | - |
| Test Target | 0 | - | - | - | - |
| Other | 0 | - | - | - | - |
Table 2: Status Statistics for SPINE by Organism
| Organism | Total Number1 | Work Stopped | Cloned | Expressed | Purified | Crystallized | Crystal Structure | NMR Structure | In PDB2 |
| Total Viruses | 149 | 1 | 89 | 33 | 11 | 6 | 7 | 0 | 2 |
| Archaea | 51 | 0 | 27 | 1 | 1 | 1 | 1 | 0 | 0 |
| Bacteria | 446 | 0 | 264 | 234 | 84 | 32 | 36 | 11 | 30 |
| Total Prokaryotes | 497 | 0 | 291 | 235 | 85 | 33 | 37 | 11 | 30 |
| Yeast | 17 | 0 | 6 | 4 | 4 | 1 | 1 | 2 | 2 |
| Fly | 6 | 0 | 3 | 1 | 1 | 0 | 0 | 0 | 0 |
| Mouse | 9 | 1 | 5 | 3 | 2 | 0 | 0 | 0 | 0 |
| Human | 379 | 1 | 214 | 178 | 78 | 27 | 24 | 14 | 27 |
| Other Eukaryotes | 38 | 0 | 25 | 20 | 16 | 5 | 5 | 1 | 6 |
| Total Eukaryotes | 449 | 2 | 253 | 206 | 101 | 33 | 30 | 17 | 35 |
| Total | 1095 | 3 | 633 | 474 | 197 | 72 | 74 | 28 | 67 |
Last updated: Aug 21 2008
Note 1:
Total counts in this table may differ from total number of targets. If targtet
is a hybrid complex
(for example:a complex of human and mouse polypeptides)
it is counted in different organism classifications.
Note 2:
Number of targets with status "in PDB". A target may reference several
PDB IDs (example: structure of the same polypeptides with different ligands).
Multiple targets in TargetDB may identify the same PDB structure when a stucture
is a result of collaboration between different centers and each center includes
the target on its target list.
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Deposited Structure Statistics for SPINE Center
Number of Released X-Ray Structures: 60
Number of Released NMR Structures: 34
Total number of released structures from SPINE center in the PDB: 94
Table 3: PDB Status Statistics for Structures from SPINE
| PDB Status | Number of Structures |
| Total Deposited | 97 |
| Released | 94 |
| Release on Publication | 0 |
| Release on Certain Date | 0 |
| In Process | 3 |
| Last updated: Aug 21 2008 |
| Note 1: "Total Deposited" are all structures in the PDB including structures released to the public and structures that are in the process to be released("Released on Publication" , "Released on Certain Date", etc.). |
Table 4: List of Structures Deposited in the PDB by SPINE
Total number of structures: 97
Structures of distinct targets: 671
1
A target may reference several PDB IDs
(example: structure of the same polypeptides with different ligands).
In this case only one structure is counted to compute number of structures of
distinct targets
Related PDB_ID(s): PDB_ID(s) associated with the same target in targetDB
| PDB_ID | Title | Target_id | Deposition Date | Released Date | PDB Status | Related PDB_ID in TargetDB |
| 1UV1 | - | CIRMMP33 | - | - | - | 1UV2 |
| 1UV2 | - | CIRMMP33 | - | - | - | none |
| ND_2 | Experimental status "in PDB", PDB ID is not provided | CIRMMP23 | - | - | - | none |
| 1XDS | crystal structure of aclacinomycin-10-hydroxylase (rdmb) in complex with s-adenosyl-l-methionine (sam) and 11-deoxy-beta-rhodomycin (dbra) | St_02 | 2004-09-08 | 2004-11-23 | REL | none |
| 1FCY | isotype selectivity of the human retinoic acid nuclear receptor hrar: the complex with the rarbeta/gamma-selective retinoid cd564 | IGBMC-0078-000 | 2000-07-19 | 2000-09-11 | REL | none |
| 1R1K | crystal structure of the ligand-binding domains of the heterodimer ecr/usp bound to ponasterone a | IGBMC-0090-000 NON-SPINE:IGBMC-0091-000 | 2003-09-24 | 2003-11-18 | REL | 1R20 |
| 2LBD | ligand-binding domain of the human retinoic acid receptor gamma bound to all-trans retinoic acid | IGBMC-0078-000 | 1997-08-19 | 1997-11-12 | REL | none |
| 1T5C | crystal structure of the motor domain of human kinetochore protein cenp-e | CENP-E_342 | 2004-05-04 | 2005-05-10 | REL | none |
| 1MVO | crystal structure of the phop receiver domain from bacillus subtilis | IGBMC-1123-000 | 2002-09-26 | 2002-10-16 | REL | none |
| 1M5T | crystal structure of the response regulator divk | IGBMC-1121-000 | 2002-07-10 | 2002-11-15 | REL | 1M5U 1MAV 1MB0 1MB3 |
| 1TXE | solution structure of the active-centre mutant ile14ala of the histidine-containing phosphocarrier protein (hpr) from staphylococcus carnosus | REGEN_HPr_Sc | 2004-07-04 | 2005-03-08 | REL | none |
| 1NM4 | solution structure of cu(i)-copc from pseudomonas syringae | CIRMMP01 | 2003-01-09 | 2003-04-08 | REL | 1OT4 |
| 2BZE | nmr structure of human rtf1 plus3 domain. | BCBRA022 | 2005-08-16 | 2007-01-03 | REL | none |
| 1P6U | nmr structure of the bef3-activated structure of the response regulator chey2-mg2+ from sinorhizobium meliloti | 1 | 2003-04-30 | 2003-11-04 | REL | none |
| 2BSY | epstein barr virus dutpase | P6-000-000-009 | 2005-05-24 | 2005-09-15 | REL | 2BT1 |
| 1OSC | crystal structure of rat cuta1 at 2.15 a resolution | CIRMMP04 | 2003-03-19 | 2003-11-25 | REL | none |
| 1FCX | isotype selectivity of the human retinoic acid nuclear receptor hrar: the complex with the rargamma-selective retinoid bms184394 | IGBMC-0078-000 | 2000-07-19 | 2000-09-11 | REL | none |
| 1ON4 | solution structure of soluble domain of sco1 from bacillus subtilis | CIRMMP02 | 2003-02-27 | 2003-11-11 | REL | none |
| 1SU3 | x-ray structure of human prommp-1: new insights into collagenase action | MPIB-401 | 2004-03-26 | 2004-12-21 | REL | none |
| 1SB6 | solution structure of a cyanobacterial copper metallochaperone, scatx1 | CIRMMP34 | 2004-02-10 | 2004-04-27 | REL | none |
| 1KA5 | refined solution structure of histidine containing phosphocarrier protein from staphyloccocus aureus | REGEN_HPr_Sa | 1995-11-20 | 1996-03-08 | REL | none |
| 1YCM | solution structure of matrix metalloproteinase 12 (mmp12) in the presence of n-isobutyl-n-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (nngh) | CIRMMP48 | 2004-12-22 | 2005-04-19 | REL | none |
| 1OLZ | the ligand-binding face of the semaphorins revealed by the high resolution crystal structure of sema4d | OPTIC7164 | 2003-08-19 | 2003-09-11 | REL | none |
| 1EXX | enantiomer discrimination illustrated by crystal structures of the human retinoic acid receptor hrargamma ligand binding domain: the complex with the inactive s-enantiomer bms270395. | IGBMC-0078-000 | 2000-05-05 | 2000-06-09 | REL | none |
| 1SJW | structure of polyketide cyclase snoal | ST_3 | 2004-03-04 | 2004-04-27 | REL | none |
| 1TW2 | crystal structure of carminomycin-4-o-methyltransferase (dnrk) in complex with s-adenosyl-l-homocystein (sah) and 4-methoxy-e-rhodomycin t (m-et) | ST_04 | 2004-06-30 | 2004-09-14 | REL | none |
| 1OQ3 | a core mutation affecting the folding properties of a soluble domain of the atpase protein copa from bacillus subtilis | CIRMMP05 | 2003-03-07 | 2003-09-16 | REL | 1OQ6 |
| 1MB3 | crystal structure of the response regulator divk at ph 8.5 in complex with mg2+ | IGBMC-1121-000 | 2002-08-02 | 2002-12-04 | REL | none |
| 1UWY | crystal structure of human carboxypeptidase m | MPIB-427 | 2004-02-17 | 2004-04-08 | REL | none |
| 1TL4 | solution structure of cu(i) hah1 | CIRMMP27 | 2004-06-09 | 2004-10-26 | REL | 1TL5 |
| 2C2I | structure and function of rv0130, a conserved hypothetical protein from m.tuberculosis | rv0130 | 2005-09-28 | 2006-09-14 | REL | none |
| 2BI0 | x-ray structure of a conserved hypothetical protein, rv0216, from mycobacterium tuberculosis. | rv0216 | 2004-12-22 | 2005-04-25 | REL | none |
| 2BF8 | crystal structure of sumo modified ubiquitin conjugating enzyme e2- 25k | SUMO | 2004-11-29 | 2005-02-16 | REL | none |
| 1QZZ | crystal structure of aclacinomycin-10-hydroxylase (rdmb) in complex with s-adensyl-l-methionine (sam) | St_02 | 2003-09-19 | 2003-11-25 | REL | 1XDS |
| 1YJU | solution structure of the apo form of the sixth soluble domain of menkes protein | CIRMMP28 | 2005-01-15 | 2006-01-03 | REL | none |
| 1FD0 | isotype selectivity of the human retinoic acid nuclear receptor hrar: the complex with the rargamma-selective retinoid sr11254 | IGBMC-0078-000 | 2000-07-19 | 2002-09-27 | REL | none |
| 1USL | structure of mycobacterium tuberculosis ribose-5-phosphate isomerase, rpib, rv2465c, complexed with phosphate. | rv2465c | 2003-11-25 | 2004-01-02 | REL | none |
| 1ZJ8 | structure of mycobacterium tuberculosis nira protein | Mtb1 | 2005-04-28 | 2005-05-31 | REL | none |
| 1QKU | wild type estrogen nuclear receptor ligand binding domain complexed with estradiol | IGBMC-0005-000 | 1999-08-05 | 2000-08-18 | REL | none |
| 2BMX | mycobacterium tuberculosis ahpc | IPRv2428PALZ | 2005-03-16 | 2005-05-10 | REL | none |
| 1YUR | solution structure of apo-s100a13 (minimized mean structure) | CIRMMP11 | 2005-02-14 | 2005-10-18 | REL | none |
| 1X9L | solution structure of cui-dr1885 from deinococcus radiodurans | CIRMMP12 | 2004-08-23 | 2004-08-31 | REL | 1X7L |
| 1BON | three-dimensional structure of bombyxin-ii, an insulin-related brain-secretory peptide of the silkmoth bombyx mori: comparison with insulin and relaxin | AF31 | 1994-07-21 | 1995-01-26 | REL | none |
| 2BDI | human kallikrein 4 complex with cobalt and p-aminobenzamidine | MPIB-209 | 2005-10-20 | 2006-10-03 | REL | none |
| 1S6O | solution structure and backbone dynamics of the apo-form of the second metal-binding domain of the menkes protein atp7a | CIRMMP25 | 2004-01-26 | 2004-04-06 | REL | 1S6U |
| 1W74 | x-ray structure of peptidyl-prolyl cis-trans isomerase a, ppia, rv0009, from mycobacterium tuberculosis. | rv0009 | 2004-08-24 | 2004-10-20 | REL | none |
| 4LBD | ligand-binding domain of the human retinoic acid receptor gamma bound to the synthetic agonist bms961 | IGBMC-0078-000 | 1998-02-04 | 1999-03-02 | REL | none |
| 1RJV | solution structure of human alpha-parvalbumin refined with a paramagnetism-based strategy | CIRMMP07 | 2003-11-20 | 2004-05-25 | REL | 1RK9 |
| 1YM3 | crystal structure of carbonic anhydrase rv3588c from mycobacterium tuberculosis | Rv3588 | 2005-01-20 | 2005-03-08 | REL | none |
| 1KV6 | x-ray structure of the orphan nuclear receptor err3 ligand-binding domain in the constitutively active conformation | IGBMC-0019-000 | 2002-01-25 | 2003-01-25 | REL | none |
| 1PFJ | solution structure of the n-terminal ph/ptb domain of the tfiih p62 subunit | IGBMC-0024-000 | 2003-05-27 | 2004-06-08 | REL | none |
| 1SW8 | solution structure of the n-terminal domain of human n60d calmodulin refined with paramagnetism based strategy | CIRMMP35 | 2004-03-30 | 2004-04-06 | REL | none |
| 1QKT | mutant estrogen nuclear receptor ligand binding domain complexed with estradiol | IGBMC-0005-000 | 1999-08-05 | 2000-08-18 | REL | none |
| 1Y3K | solution structure of the apo form of the fifth domain of menkes protein | CIRMMP26 | 2004-11-25 | 2005-03-08 | REL | none |
| 1OQ6 | solution structure of copper-s46v copa from bacillus subtilis | CIRMMP05 | 2003-03-07 | 2003-09-16 | REL | none |
| 1EXA | enantiomer discrimination illustrated by crystal structures of the human retinoic acid receptor hrargamma ligand binding domain: the complex with the active r-enantiomer bms270394. | IGBMC-0078-000 | 2000-05-02 | 2000-06-09 | REL | 1EXX 1FCX 1FCY 1FCZ 1FD0 2LBD 3LBD 4LBD |
| 1G50 | crystal structure of a wild type her alpha lbd at 2.9 angstrom resolution | IGBMC-0005-000 | 2000-10-30 | 2002-02-06 | REL | 1QKT 1QKU |
| 1XA3 | crystal structure of caib, a type iii coa transferase in carnitine metabolism | AD59 | 2004-08-25 | 2004-11-16 | REL | none |
| 1UB1 | solution structure of the matrix attachment region-binding domain of chicken mecp2 | 3 | 2003-03-27 | 2003-08-05 | REL | none |
| 1YJR | solution structure of the apo form of the sixth soluble domain a69p mutant of menkes protein | CIRMMP29 | 2005-01-15 | 2006-01-03 | REL | none |
| 1Q0Z | crystal structure of aclacinomycin methylesterase (rdmc) with bound product analogue, 10-decarboxymethylaclacinomycin a (dcma) | St_1 | 2003-07-18 | 2003-11-25 | REL | none |
| 2BEP | crystal structure of ubiquitin conjugating enzyme e2-25k | Hip2 | 2004-11-25 | 2005-02-16 | REL | none |
| 2BDG | human kallikrein 4 complex with nickel and p-aminobenzamidine | MPIB-209 | 2005-10-20 | 2006-10-03 | REL | 2BDH 2BDI |
| 1FCZ | isotype selectivity of the human retinoic acid nuclear receptor hrar: the complex with the panagonist retinoid bms181156 | IGBMC-0078-000 | 2000-07-19 | 2000-09-11 | REL | none |
| 1UVQ | crystal structure of hla-dq0602 in complex with a hypocretin peptide | OPTIC7172 | 2004-01-22 | 2004-02-05 | REL | none |
| 1YJE | crystal structure of the rngfi-b ligand-binding domain | IGBMC-1013-000 | 2005-01-14 | 2005-02-22 | REL | none |
| 1MAV | crystal structure of the response regulator divk at ph 6.0 in complex with mn2+ | IGBMC-1121-000 | 2002-08-02 | 2002-12-04 | REL | none |
| 3LBD | ligand-binding domain of the human retinoic acid receptor gamma bound to 9-cis retinoic acid | IGBMC-0078-000 | 1998-02-04 | 1999-03-02 | REL | none |
| 1SZW | crystal structure of e. coli trna pseudouridine synthase trud | AF46 | 2004-04-06 | 2004-04-20 | REL | none |
| 1UOS | the crystal structure of the snake venom toxin convulxin | OX_CVX | 2003-09-22 | 2003-10-14 | REL | none |
| 1LBD | ligand-binding domain of the human nuclear receptor rxr-alpha | IGBMC-0017-000 | 1996-05-22 | 1996-11-08 | REL | none |
| 2BDH | human kallikrein 4 complex with zinc and p-aminobenzamidine | MPIB-209 | 2005-10-20 | 2006-10-03 | REL | none |
| 1YLK | crystal structure of rv1284 from mycobacterium tuberculosis in complex with thiocyanate | Rv1284 | 2005-01-19 | 2005-03-08 | REL | none |
| 1P6Q | nmr structure of the response regulator chey2 from sinorhizobium meliloti, complexed with mg++ | 1 | 2003-04-30 | 2004-06-15 | REL | 1P6U |
| 1TTX | solution stucture of human beta parvalbumin (oncomodulin) refined with a paramagnetism based strategy | CIRMMP08 | 2004-06-23 | 2005-01-18 | REL | none |
| 2BT1 | epstein barr virus dutpase in complex with a,b-imino dutp | P6-000-000-009 | 2005-05-24 | 2005-09-15 | REL | none |
| 1S6U | solution structure and backbone dynamics of the cu(i) form of the second metal-binding domain of the menkes protein atp7a | CIRMMP25 | 2004-01-27 | 2004-04-06 | REL | none |
| 1O6Y | catalytic domain of pknb kinase from mycobacterium tuberculosis | IPRv0014cPALZ TB:Rv0014c | 2002-10-21 | 2003-01-30 | REL | none |
| 1SO9 | solution structure of apocox11, 30 structures | CIRMMP18 | 2004-03-13 | 2004-08-10 | REL | none |
| 1P6T | structure characterization of the water soluble region of p-type atpase copa from bacillus subtilis | CIRMMP06 | 2003-04-30 | 2003-12-16 | REL | none |
| 1OT4 | solution structure of cu(ii)-copc from pseudomonas syringae | CIRMMP01 | 2003-03-21 | 2003-07-08 | REL | none |
| 2BNG | structure of an m.tuberculosis leh-like epoxide hydrolase | rv2740 | 2005-03-24 | 2005-08-03 | REL | none |
| 1DKF | crystal structure of a heterodimeric complex of rar and rxr ligand-binding domains | IGBMC-0012-000 | 1999-12-07 | 2000-04-19 | REL | none |
| 1O6E | epstein-barr virus protease | P6-000-000-014 | 2002-09-13 | 2002-11-14 | REL | none |
| 1TL5 | solution structure of apohah1 | CIRMMP27 | 2004-06-09 | 2004-10-26 | REL | none |
| 1MB0 | crystal structure of the response regulator divk at ph 8.0 in complex with mn2+ | IGBMC-1121-000 | 2002-08-02 | 2002-12-04 | REL | none |
| 1NAQ | crystal structure of cuta1 from e.coli at 1.7 a resolution | CIRMMP03 | 2002-11-28 | 2003-11-25 | REL | none |
| 1M5U | crystal structure of the response regulator divk. structure at ph 8.0 in the apo-form | IGBMC-1121-000 | 2002-07-10 | 2002-11-15 | REL | none |
| 1G2N | crystal structure of the ligand binding domain of the ultraspiracle protein usp, the ortholog of rxrs in insects | IGBMC-0091-000 | 2000-10-20 | 2001-04-21 | REL | 1R1K 1R20 |
| 1Q0R | crystal structure of aclacinomycin methylesterase (rdmc) with bound product analogue, 10-decarboxymethylaclacinomycin t (dcmat) | St_1 | 2003-07-17 | 2003-11-25 | REL | 1Q0Z |
| 1W6V | solution structure of the dusp domain of husp15 | BCBRA016 | 2004-08-24 | 2006-01-12 | REL | none |
| 1ZT4 | the crystal structure of human cd1d with and without alpha-galactosylceramide | CD1d_cell_surface_antigen | 2005-05-26 | 2005-07-19 | REL | none |
| 1Y3J | solution structure of the copper(i) form of the fifth domain of menkes protein | CIRMMP26 | 2004-11-25 | 2005-03-08 | REL | 1Y3K |
| 1R20 | crystal structure of the ligand-binding domains of the heterodimer ecr/usp bound to the synthetic agonist byi06830 | IGBMC-0090-000 NON-SPINE:IGBMC-0091-000 | 2003-09-25 | 2003-11-18 | REL | none |
| 1RK9 | solution structure of human alpha-parvalbumin (minimized average structure) | CIRMMP07 | 2003-11-21 | 2004-06-08 | REL | none |
| 1Q7X | solution structure of the alternatively spliced pdz2 domain (pdz2b) of ptp-bas (hptp1e) | 2 | 2003-08-20 | 2003-12-02 | REL | none |
| 1X7L | solution structure of apo-dr1885 from deinococcus radiodurans | CIRMMP12 | 2004-08-16 | 2004-08-31 | Replaced by:2JQA | none |
Note 1: Last updated: Aug 21 2008
back to topSequence Redundancy Statistics
Table 5: Sequence Redundancy Statistics for SPINE by Experimental Status
| Sequence Identity(%) | Novel Targets
Status: Selected |
Novel Targets Status: Cloned |
Novel Targets Status: Expressed |
Novel Targets Status: Purified |
Novel Targets Status: Crystallized |
Novel Targets Status: Crystal Structure | Novel Targets Status: NMR Structure | Novel Targets Status: in PDB |
| <100 | 971 | 593 | 444 | 191 | 68 | 70 | 28 | 67 |
| <90 | 944 | 585 | 439 | 188 | 68 | 70 | 25 | 64 |
| <70 | 926 | 576 | 433 | 185 | 65 | 67 | 25 | 63 |
| <50 | 859 | 550 | 416 | 175 | 64 | 64 | 24 | 60 |
| <30 | 590 | 416 | 334 | 151 | 57 | 58 | 21 | 51 |
| Last updated: 08-04-08 |
| Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity. Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings. Sequence redundancy calculations are based on comparison to all protein sequences in TargetDB which are in the same experimental status category and at least 20 amino acids long |
Table 6:Sequence Redundancy Statistics for Structures Released by SPINE by Year
| Year | Released Structures | Number of Released Structures <30% Identity at Time of Release | Percent(%) of Released Structures <30% Identity(%) at Time of Release |
| <= 2000 | 14 | 0 | 0 |
| 2001 | 1 | 0 | 0 |
| 2002 | 9 | 0 | 0 |
| 2003 | 20 | 4 | 20 |
| 2004 | 23 | 7 | 30 |
| 2005 | 19 | 5 | 26 |
| 2006 | 7 | 1 | 14 |
| 2007 | 1 | 0 | 0 |
| Total | 94 | 17 | 18 |
| Last updated:08-08-21 |
| Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity. Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings. Sequence redundancy calculations are based on comparison to all protein sequences in the PDB which are at least 20 amino acids long |