3PW3 | pdb_00003pw3

Crystal structure of a cysteine protease (BDI_2249) from Parabacteroides distasonis ATCC 8503 at 2.23 A resolution

PDB DOI: https://doi.org/10.2210/pdb3PW3/pdb

Classification: HYDROLASE
Organism(s): Parabacteroides distasonis ATCC 8503
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-07 Released: 2010-12-22
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.181 (Depositor), 0.180 (DCC)
R-Value Work:
0.159 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a cysteine protease (BDI_2249) from Parabacteroides distasonis ATCC 8503 at 2.23 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 267.73 kDa
Atom Count: 19,429
Modeled Residue Count: 2,162
Deposited Residue Count: 2,298
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase C	A, B, C, D, E A, B, C, D, E, F	383	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_2249
UniProt
Find proteins for A6LE66 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LE66 Go to UniProtKB: A6LE66
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6LE66
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain OA [auth F] SDF format, chain Z [auth C] SDF format, chain Q [auth B] SDF format, chain JA [auth E] SDF format, chain G [auth A] SDF format, chain EA [auth D] MOL2 format, chain OA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain JA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain OA [auth F] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain JA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth D]	EA [auth D] G [auth A] JA [auth E] OA [auth F] Q [auth B] EA [auth D], G [auth A], JA [auth E], OA [auth F], Q [auth B], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain G [auth A] Focus chain JA [auth E] Focus chain OA [auth F] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain G [auth A] Focus chain JA [auth E] Focus chain OA [auth F] Focus chain Q [auth B] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain IA [auth D] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain UA [auth F] SDF format, chain TA [auth F] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain DA [auth C]	CA [auth C] DA [auth C] IA [auth D] K [auth A] L [auth A] CA [auth C], DA [auth C], IA [auth D], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], TA [auth F], UA [auth F], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain W [auth B] Focus chain X [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain VA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain VA [auth F] mmCIF format, chain Y [auth B] mmCIF format, chain VA [auth F]	VA [auth F], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain VA [auth F] Focus chain Y [auth B] Interactions & Density Focus chain VA [auth F] Focus chain Y [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain H [auth A] SDF format, chain KA [auth E] SDF format, chain R [auth B] SDF format, chain QA [auth F] SDF format, chain PA [auth F] SDF format, chain I [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D]	AA [auth C] BA [auth C] FA [auth D] GA [auth D] H [auth A] AA [auth C], BA [auth C], FA [auth D], GA [auth D], H [auth A], I [auth A], KA [auth E], PA [auth F], QA [auth F], R [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth E] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth E] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain NA [auth E] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain SA [auth F] SDF format, chain RA [auth F] SDF format, chain MA [auth E] SDF format, chain LA [auth E] SDF format, chain J [auth A] SDF format, chain HA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain MA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth D] mmCIF format, chain NA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain MA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth D]	HA [auth D] J [auth A] LA [auth E] MA [auth E] NA [auth E] HA [auth D], J [auth A], LA [auth E], MA [auth E], NA [auth E], RA [auth F], S [auth B], SA [auth F], T [auth B], U [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth D] Focus chain J [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain HA [auth D] Focus chain J [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]