Statistics Summary Report for NYCOMPS Center

Last updated: Mar 11 2010

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

Target Status Statistics

Total number of targets deposited by NYCOMPS to TargetDB: 9343

      View NYCOMPS Target List

Table 1: Status Statistics for NYCOMPS

Status	Total Number of Targets	(%) Relative to "Cloned" Targets	(%) Relative to "Expressed" Targets	(%) Relative to "Purified" Targets	(%) Relative to "Crystallized" Targets
Cloned	8630	100.0	-	-	-
Expressed	2669	30.9	100.0	-	-
Soluble	277	3.2	10.4	-	-
Purified	603	7.0	22.6	100.0	-
Crystallized	3	0.0	0.1	0.5	100.0
Diffraction-quality Crystals	5	0.1	0.2	0.8	166.7
Diffraction	4	0.0	0.1	0.7	133.3
NMR Assigned	0	0.0	0.0	0.0	-
HSQC	0	0.0	0.0	0.0	-
Crystal Structure	2	0.0	0.1	0.3	66.7
NMR Structure	0	0.0	0.0	0.0	-
In PDB1	4	0.0	0.1	0.7	133
Work Stopped	6861	-	-	-	-
Test Target	0	-	-	-	-
Other	495	-	-	-	-

Last updated: Mar 11 2010

Table 2: Status Statistics for NYCOMPS 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	6	3	6	3	2	0	0	0	0
Archaea	916	733	788	181	30	1	0	0	1
Bacteria	8338	6123	7753	2486	572	2	2	0	3
Prokaryota	9254	6856	8541	2667	602	3	2	0	4
Yeast	23	0	23	0	0	0	0	0	0
Trypanosoma	15	0	15	0	0	0	0	0	0
Drosophila	20	0	20	0	0	0	0	0	0
Mouse	3	0	3	0	0	0	0	0	0
Human	23	0	23	0	0	0	0	0	0
Eukaryota	96	12	96	3	0	0	0	0	0
Uncultured or unidentified	2	1	2	1	0	0	0	0	0

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 NYCOMPS Center

Number of Released X-Ray Structures: 8

Number of Released NMR Structures: 0

Total number of released structures from NYCOMPS center in the PDB: 8

Table 3: PDB Status Statistics for Structures from NYCOMPS

PDB Status	Number of Structures
Total Deposited	8
Released	8
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 NYCOMPS

Total number of structures: 8

Structures of distinct targets: 41

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
3GI8	crystal structure of apct k158a transporter bound to 7f11 monoclonal fab fragment	GO.9411	2009-03-05	2009-08-18	REL	3GI9 3GIA
3K3F	crystal structure of the urea transporter from desulfovibrio vulgaris	GO.3782	2009-10-02	2009-11-17	REL	3K3G
3GIA	crystal structure of apct transporter	GO.9411	2009-03-05	2009-08-18	REL	none
3K3G	crystal structure of the urea transporter from desulfovibrio vulgaris bound to 1,3-dimethylurea	GO.3782	2009-10-02	2009-11-17	REL	none
3KLY	pentameric formate channel	GO.190	2009-11-09	2009-12-15	REL	3KLZ
3GI9	crystal structure of apct transporter bound to 7f11 monoclonal fab fragment	GO.9411	2009-03-05	2009-08-18	REL	none
3KLZ	pentameric formate channel with formate bound	GO.190	2009-11-09	2009-12-15	REL	none
2QJU	crystal structure of an nss homolog with bound antidepressant	GO.3204	2007-07-09	2007-08-21	REL	none

Note 1:  Last updated: Mar 11 2010

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Sequence Redundancy Statistics

Table 5: Sequence Redundancy Statistics for NYCOMPS 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	6372	2945	2076	408	0	0	1
<90	5915	2743	1985	397	0	0	1
<70	4926	2288	1727	373	0	0	1
<50	3249	1550	1287	315	0	0	1
<30	816	493	483	169	0	0	1

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 NYCOMPS 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
2007	1	0	0
2009	7	2	29
Total	8	2	25

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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