Statistics Summary Report for SGPP Center

Last updated: Mar 11 2010

• Target Status Statistics
  • Table 1: Status Statistics for SGPP
  • Table 2: Status Statistics for SGPP by Organisms
• Deposited Structure Statistics
  • Table 3: PDB Status Statistics for Structures from SGPP
  • Table 4: List of Structures Deposited by SGPP in the PDB
• Sequence Redundancy Statistics
  • Table 5: Sequence Redundancy Statistics for SGPP by Experimental Status
  • Table 6: Sequence Redundancy Statistics for Structures Released by SGPP in the PDB by Year

Target Status Statistics

Total number of targets deposited by SGPP to TargetDB: 20854

      View SGPP Target List

Table 1: Status Statistics for SGPP

Status	Total Number of Targets	(%) Relative to "Cloned" Targets	(%) Relative to "Expressed" Targets	(%) Relative to "Purified" Targets	(%) Relative to "Crystallized" Targets
Cloned	11228	100.0	-	-	-
Expressed	5296	47.2	100.0	-	-
Soluble	1624	14.5	30.7	-	-
Purified	887	7.9	16.7	100.0	-
Crystallized	267	2.4	5.0	30.1	100.0
Diffraction-quality Crystals	104	0.9	2.0	11.7	39.0
Diffraction	61	0.5	1.2	6.9	22.8
NMR Assigned	0	0.0	0.0	0.0	-
HSQC	0	0.0	0.0	0.0	-
Crystal Structure	47	0.4	0.9	5.3	17.6
NMR Structure	0	0.0	0.0	0.0	-
In PDB1	41	0.4	0.8	4.6	15
Work Stopped	609	-	-	-	-
Test Target	0	-	-	-	-
Other	0	-	-	-	-

Last updated: Mar 11 2010

Table 2: Status Statistics for SGPP by Organism

These statistics are derived from mapping of target sequences to GenBank using >=98% sequence identity cut off

Organism	Total Number1	Work Stopped	Cloned	Expressed	Purified	Crystallized	Crystal Structure	NMR Structure	In PDB2
Viruses	3	0	2	1	0	0	0	0	0
Bacteria	28	4	12	3	0	0	0	0	0
Prokaryota	28	4	12	3	0	0	0	0	0
Plasmodium	4637	255	2555	1141	177	60	16	0	16
Trypanosoma	5226	47	3385	1723	285	55	9	0	7
Leishmania	8648	271	4161	2110	368	139	20	0	16
Drosophila	1	1	1	1	0	0	0	0	0
Mouse	1	1	1	1	0	0	0	0	0
Human	5	1	3	1	0	0	0	0	0
Eukaryota	18436	573	10023	4881	830	254	45	0	39

Last updated: Mar 11 2010

Note 1:   Total counts in this table may differ from total number of targets and structures. A target is counted in different organism specifications if:
- a target is mapped to different organisms
- a targtet is a hybrid complex (for example:a complex of human and mouse polypeptides)

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Deposited Structure Statistics for SGPP Center

Number of Released X-Ray Structures: 41

Number of Released NMR Structures: 0

Total number of released structures from SGPP center in the PDB: 41

Table 3: PDB Status Statistics for Structures from SGPP

PDB Status	Number of Structures
Total Deposited	41
Released	41
In Process	0

Last updated: Mar 11 2010

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 SGPP

Total number of structures: 41

Structures of distinct targets: 411

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
1TC5	structural analysis of a probable eukaryotic d-amino acid trna deacylase	Lmaj005534AAA	2004-05-20	2004-06-08	REL	none
2B4G	dihydroorotate dehydrogenase	Tbru015978AAA	2005-09-23	2005-10-11	REL	none
2A0U	crystal structure of the eukaryotic initiation factor 2b from leishmania major at 2.1 a resolution	Lmaj006238AAA	2005-06-17	2005-08-02	REL	none
1YZV	hypothetical protein from trypanosoma cruzi	Tcru003547AAA	2005-02-28	2005-03-08	REL	none
1XQ9	structure of phosphoglycerate mutase from plasmodium falciparum at 2.6 resolution	Pfal005984AAA	2004-10-11	2004-12-21	REL	none
1Y13	structural analysis of plasmodium falciparum 6-pyruvoyl tetrahydropterin synthase (ptps)	Pfal004546AAA	2004-11-17	2005-01-04	REL	none
1TQX	crystal structure of pfal009167 a putative d-ribulose 5-phosphate 3-epimerase from p.falciparum	Pfal009167AAA	2004-06-18	2004-12-21	REL	none
1YF9	structural analysis of leishmania major ubiquitin conjugating enzyme e2	Lmaj005461AAB	2004-12-31	2005-02-22	REL	none
1R75	leishmania major hypothetical protein	Lmaj002144AAA	2003-10-17	2003-12-02	REL	none
2B4W	hypothetical protein from leishmania major	Lmaj006873AAA	2005-09-26	2005-10-04	REL	none
1X9G	putative mar1 ribonuclease from leishmania donovani	Ldon001686AAA	2004-08-20	2004-09-07	REL	none
2F8M	ribose 5-phosphate isomerase from plasmodium falciparum	Pfal008434AAA	2005-12-02	2005-12-27	REL	none
1YJ8	initial structural analysis of plasmodium falciparum glycerol-3-phosphate dehydrogenase	Pfal009132AAA	2005-01-13	2005-02-01	REL	none
2A0M	arginase superfamily protein from trypanosoma cruzi	Tcru010945AAA	2005-06-16	2005-07-05	REL	none
2AR1	structure of hypothetical protein from leishmania major	Lmaj006129AAA	2005-08-18	2005-08-30	REL	none
1XTD	structural analysis of leishmania mexicana eukaryotic initiation factor 5a	Lmex003024AAA	2004-10-21	2004-10-26	REL	none
2B30	initial crystallographic structural analysis of a putative had/cof-like hydrolase from plasmodium vivax	Pviv002324AAA	2005-09-19	2005-09-27	REL	none
1XN4	putative mar1 ribonuclease from leishmania major	Lmaj001686AAA	2004-10-04	2004-10-12	REL	none
2A03	superoxide dismutase protein from plasmodium berghei	Pber005319AAA	2005-06-15	2005-06-21	REL	none
1YQF	hypothetical protein from leishmania major unknown function sequence homologue to human p32 protein	Lmaj011689AAA	2005-02-01	2005-02-22	REL	none
1VJQ	designed protein based on backbone conformation of procarboxypeptidase-a (1aye) with sidechains chosen for maximal predicted stability.	DBsf000001AYE	2004-03-19	2004-03-30	REL	none
1Y1X	structural analysis of a homolog of programmed cell death 6 protein from leishmania major friedlin	Lmaj01134AAC	2004-11-19	2004-12-07	REL	none
2B94	structural analysis of p knowlesi homolog of p falciparum pnp	Pkno008421AAA	2005-10-10	2005-11-01	REL	none
1Y63	initial crystal structural analysis of a probable kinase from leishmania major friedlin	Lmaj004144AAA	2004-12-03	2005-01-04	REL	none
1VJU	coproporphyrinogen iii oxidase from leishmania major	Lmaj006828AAA	2004-03-29	2004-04-13	REL	none
1ZSO	hypothetical protein from plasmodium falciparum	Pfal004331AAA	2005-05-24	2005-06-07	REL	none
2AMH	crystal structure of maf-like protein tbru21784aaa from t.brucei	Tbru021784AAA	2005-08-09	2005-08-16	REL	none
2Q0X	alpha/beta hydrolase fold protein of unknown function	Tbru020260AAA	2007-05-22	2007-06-26	REL	none
1XO7	crystal structure of cyclophilin from trypanosoma cruzi	Tcru013382AAA	2004-10-05	2004-12-21	REL	none
2B4R	crystal structure of glyceraldehyde-3-phosphate dehydrogenase from plasmodium falciparum at 2.25 angstrom resolution reveals intriguing extra electron density in the active site	Pfal007254AAA	2005-06-09	2005-07-26	REL	none
1X6O	structural analysis of leishmania braziliensis eukaryotic initiation factor 5a	Lbra003024AAA	2004-08-11	2004-08-24	REL	none
1XIQ	plasmodium falciparum nucleoside diphosphate kinase b	Pfal006645AAA	2004-09-21	2004-10-12	REL	none
1SYR	initial structural analysis of plasmodium falciparum thioredoxin	Pfal007201AAA	2004-04-01	2004-04-13	REL	none
1SVV	initial stuctural analysis of leishmania major threonine aldolase	Lmaj008024AAA	2004-03-30	2004-08-17	REL	none
2HQJ	cyclophilin from leishmania major	Lmaj007771BAB	2006-07-18	2006-07-25	REL	none
1SQ6	plasmodium falciparum homolog of uridine phosphorylase/purine nucleoside phosphorylase	Pfal008421AAA	2004-03-17	2004-04-06	REL	none
2A0S	crystal structure of 6-pyruvoyl tetrahydropterin synthase (ptps) from plasmodium vivax at 2.2 a resolution	Pviv004546AAA	2005-06-16	2005-07-26	REL	none
2GZQ	phosphatidylethanolamine-binding protein from plasmodium vivax	Pviv009166AAA	2006-05-11	2006-05-23	REL	none
1XTP	structural analysis of leishmania major lmaj004091aaa, a sam-dependent methyltransferase of the duf858/pfam05891 family	Lmaj004091AAA	2004-10-22	2004-11-09	REL	none
2F84	crystal structure of an orotidine-5'-monophosphate decarboxylase homolog from p.falciparum	Pfal000304AAA	2005-12-01	2005-12-20	REL	none
2A0K	crystal structure of nucleoside 2-deoxyribosyltransferase from trypanosoma brucei at 1.8 a resolution	Tbru015777AAA	2005-06-16	2005-07-26	REL	none

Note 1:  Last updated: Mar 11 2010

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Sequence Redundancy Statistics

Table 5: Sequence Redundancy Statistics for SGPP 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: in PDB
<100	14834	8582	3927	743	224	45	40
<90	13624	8106	3750	714	212	44	39
<70	12605	7557	3597	687	206	43	38
<50	11099	6838	3351	642	193	39	35
<30	8656	5673	2950	577	184	39	35

Last updated: 10-03-08

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 SGPP 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
2003	1	1	100
2004	16	4	25
2005	21	8	38
2006	2	1	50
2007	1	1	100
Total	41	15	37

Last updated:10-03-11

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

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