ccPDB: Compilation and Creation of Datasets from PDB

This page provides datasets compiled from release of PDB (31st July 2011). These datasets were generated using commonly used protocols like non-redundant chains, structures solved at high resolution. Compilation of more datasets in progress. For more information click help.

Types of Datasets	Description of Dataset	NR chains	No. of residues	Download
Secondary structure (assign using DSSP database, chains using PDB select)	Eight state (H,B,E,G,I,T,S,C) Three state [H=(G,H,I); E=(B,E); C=(T,S)] Three state [H=H; E=E; C=(G,I,B,T,S)]	5130 5130 5130		DSSP8 DSSP3_1 DSSP3_2 Data Description
Irregular Secondary structure Mainly Tight Turns (Promotif used for assignment)	Beta-Turns I Beta-Turns I' Beta-Turns II Beta-Turns II' Beta-Turns VI Beta-Turns VIa1 Beta-Turns VIa2 Beta-Turns VIb Beta-Turns VIII	6132 2907 4967 2118 6068 596 195 944 4454	147246 18603 55487 11365 138501 2596 814 4424 41769	BTI6132 BTI'2907 BTII4967 BTII'2118 BTIV6068 BTVIa1_596 BTVIa2_195 BTVIb944 BTVIII4454 Data Description
	Gamma-turn-C Gamma-turn-I	974 5401	3261 39114	GT974 GT5401 Data Description
	Buldge-B Buldge-C Buldge-G Bulge-S Buldge-W	252 4542 3389 657 797	767 33489 20335 2940 2890	BLGB252 BLGC4542 BLGG3389 BLGS657 BLGW797
	Hairpin	4799	167865	HPIN4799
	Psiloop	1092	21502	PLOOP1092
DNA/RNA interacting residues	DNA RNA	451 307	11471 9747	DNA451 RNA307
DNA/RNA interacting proteins	DNA RNA	451 307		DNA451 RNA307
Nucleotide interacting residuess	ATP ADP GTP GDP NAD FAD FMN UDP	219 289 51 85 128 146 99 49	2943 3900 625 1013 2464 3491 1575 618	ATP219 ADP289 GTP51 GDP85 NAD128 FAD146 FMN99 UDP49
Nucleotide interacting Proteins	ATP ADP GTP GDP NAD FAD FMN UDP	219 289 51 85 128 146 99 49		ATP219 ADP289 GTP51 GDP85 NAD128 FAD146 FMN99 UDP49
Ligand binding residues	Sulphate Phosphate NAG HEM BME EDO PLP	2472 937 453 165 156 1009 64	17802 5822 3730 4062 870 12475 801	SO4_2472 PO4_937 NAG453 HEM165 BME156 EDO1009 PLP64
Ligand binding proteins	Sulphate Phosphate NAG HEM BME EDO PLP	2472 937 453 165 156 1009 64		SO4_2472 PO4_937 NAG453 HEM165 BME156 EDO1009 PLP64
Metal interacting residues	Fe Mg Ca Mn Zn Co Ni	157 1322 973 366 1078 202 355	665 3991 3791 1467 5166 563 661	Fe157 MG1322 CA973 MN366 ZN1078 CO202 NI355
Metal interacting proteins	Fe Mg Ca Mn Zn Co Ni	157 1322 973 366 1078 202 355		Fe157 MG1322 CA973 MN366 ZN1078 CO202 NI355

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Datasets compiled from PDB (31st Jan 2012)

This page provides datasets compiled from release of PDB (31st Jan 2012). These datasets were generated using commonly used protocols like non-redundant chains, structures solved at high resolution. Compilation of more datasets in progress. For more information click help. Archive datasets.

Types of Datasets	Description of Dataset	NR chains	No. of residues	Download
Secondary structure (assign using DSSP database, chains using PDB select)	Eight state (H,B,E,G,I,T,S,C) Three state [H=(G,H,I); E=(B,E); C=(T,S)] Three state [H=H; E=E; C=(G,I,B,T,S)]	5807 5807 5807		DSSP8 DSSP3_1 DSSP3_2 Data Description
Irregular Secondary structure Mainly Tight Turns (Promotif used for assignment)	Beta-Turns I Beta-Turns I' Beta-Turns II Beta-Turns II' Beta-Turns VI Beta-Turns VIa1 Beta-Turns VIa2 Beta-Turns VIb Beta-Turns VIII	4844 2246 3843 1628 4794 494 140 726 3473	108669 14211 41303 8673 101313 2143 582 3381 30912	BTI4844 BTI'2246 BTII3843 BTII'1628 BTIV4794 BTVIa1_494 BTVIa2_140 BTVIb726 BTVIII3473 Data Description
	Gamma-turn-C Gamma-turn-I	654 3823	2180 27901	GT654 GT3823 Data Description
	Buldge-B Buldge-C Buldge-G Bulge-S Buldge-W	177 3505 2596 488 596	533 25602 15293 2180 2152	BLGB177 BLGC3505 BLGG25963389 BLGS488 BLGW596
	Hairpin	3656	130502	HPIN3656
	Psiloop	783	14333	PLOOP783
DNA/RNA interacting residues	DNA RNA	467 312	12771 10706	DNA467 RNA312
DNA/RNA interacting proteins	DNA RNA	467 312		DNA467 RNA312
Nucleotide interacting residuess	ATP ADP GTP GDP NAD FAD FMN UDP	223 294 52 85 129 147 101 50	3008 3966 639 1013 2472 3505 1609 628	ATP223 ADP294 GTP52 GDP85 NAD129 FAD147 FMN101 UDP50
Nucleotide interacting Proteins	ATP ADP GTP GDP NAD FAD FMN UDP	223 294 52 85 129 147 101 50		ATP223 ADP294 GTP52 GDP85 NAD129 FAD147 FMN101 UDP50
Ligand binding residues	Sulphate Phosphate NAG HEM BME EDO PLP	2503 948 462 165 157 1024 65	18074 5881 3779 4109 884 12655 814	SO4_2503 PO4_948 NAG462 HEM165 BME157 EDO1024 PLP65
Ligand binding proteins	Sulphate Phosphate NAG HEM BME EDO PLP	2503 948 462 165 157 1024 65		SO4_2503 PO4_948 NAG462 HEM165 BME157 EDO1024 PLP65
Metal interacting residues	Fe Mg Ca Mn Zn Co Ni	158 1332 982 371 1091 143 229	676 4020 3854 1482 5230 588 681	Fe158 MG1322 CA982 MN371 ZN1091 CO413 NI229
Metal interacting proteins	Fe Mg Ca Mn Zn Co Ni	158 1332 982 371 1091 143 229		Fe158 MG1322 CA982 MN371 ZN1091 CO143 NI229


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Datasets compiled from PDB (31st July 2011)

Datasets compiled from PDB (31st Jan 2012)