Statistics Summary Report for NYCOMPS Center

Last updated: Feb 2 2012

• 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: 12510

      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	8966	100.0	-	-	-
Expressed	2699	30.1	100.0	-	-
Soluble	461	5.1	17.1	-	-
Purified	820	9.1	30.4	100.0	-
Crystallized	9	0.1	0.3	1.1	100.0
Diffraction-quality Crystals	9	0.1	0.3	1.1	100.0
Diffraction	2	0.0	0.1	0.2	22.2
NMR Assigned	0	0.0	0.0	0.0	-
HSQC	0	0.0	0.0	0.0	-
Crystal Structure	7	0.1	0.3	0.9	77.8
NMR Structure	0	0.0	0.0	0.0	-
In PDB1	9	0.1	0.3	1.1	100
Work Stopped	9675	-	-	-	-
Test Target	0	-	-	-	-
Other	510	-	-	-	-

Last updated: Feb 2 2012

Note 1:   Number of targets with status "in PDB" may not be equal to number of structures determined by a project. 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.

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 PDB
Viruses	6	3	5	4	2	0	0	0	0
Archaea	1250	1068	869	167	41	1	1	0	1
Bacteria	10804	8536	7853	2518	777	8	6	0	8
Prokaryota	12054	9604	8722	2685	818	9	7	0	9
Yeast	23	7	15	0	0	0	0	0	0
Plasmodium	9	0	0	0	0	0	0	0	0
Trypanosoma	15	10	5	0	0	0	0	0	0
Arabidopsis	2	0	0	0	0	0	0	0	0
Worm	1	0	0	0	0	0	0	0	0
Drosophila	22	13	7	0	0	0	0	0	0
Mouse	238	5	141	0	0	0	0	0	0
Human	85	16	54	6	0	0	0	0	0
Eukaryota	456	72	235	15	4	0	0	0	0
Uncultured or unidentified	5	2	5	3	1	0	0	0	0

Last updated: Feb 2 2012

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 target 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: 26

Number of Released NMR Structures: 0

Total number of released structures from NYCOMPS center in the PDB: 26

Table 3: PDB Status Statistics for Structures from NYCOMPS

PDB Status	Number of Structures
Total Deposited	26
Released	26
In Process	0

Last updated: Feb 2 2012

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: 26

Structures of distinct targets: 91

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
3M7B	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
3M73	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
3M75	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
3M6E	f80a mutant of the urea transporter from desulfovibrio vulgaris	GO.3782	2010-03-15	2010-08-04	REL	none
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
3QNQ	crystal structure of the transporter chbc, the iic component from the n,n'-diacetylchitobiose-specific phosphotransferase system	GO.83	2011-02-08	2011-04-06	REL	none
3M77	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
3M7L	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
2QJU	crystal structure of an nss homolog with bound antidepressant	GO.3204	2007-07-09	2007-08-21	REL	none
3M71	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	3M72 3M73 3M74 3M75 3M76 3M77 3M78 3M7B 3M7C 3M7E 3M7L
3M7C	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
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 3M6E 3ME1
3M7E	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
3M72	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
3PJZ	crystal structure of the potassium transporter trkh from vibrio parahaemolyticus	GO.1008	2010-11-10	2011-01-19	REL	none
3M74	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
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
3M76	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none
3LLQ	aquaporin structure from plant pathogen agrobacterium tumerfaciens	GO.11661	2010-01-29	2010-02-16	REL	none
3ME1	crystal structure of the desulfovibro vulgaris urea transporter in the p3(1) space group at 3.86	GO.3782	2010-03-31	2011-01-19	REL	none
3M70	crystal structure of tehb from haemophilus influenzae	GO.11668	2010-03-16	2010-05-12	REL	none
3M78	crystal structure of plant slac1 homolog teha	GO.8497	2010-03-16	2010-05-12	REL	none

Last updated: Feb 2 2012

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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	11689	8395	2625	818	9	7	9
<98	11597	8325	2610	815	9	7	9
<95	11288	8158	2576	812	9	7	9
<90	10949	7943	2525	802	9	7	9
<70	9401	6922	2245	743	9	7	9
<50	6576	5037	1739	628	9	7	9
<40	4577	3590	1316	514	9	7	9
<30	2475	2038	778	361	9	7	9

Last updated: 12-01-10

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
2010	15	1	7
2011	3	2	67
Total	26	5	19

Last updated: 12-02-02

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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