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), 0.181 (DCC)
R-Value Work:
0.159 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3PW3

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Z [auth C] SDF format, chain Q [auth B] SDF format, chain OA [auth F] SDF format, chain JA [auth E] SDF format, chain G [auth A] SDF format, chain EA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain JA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth F] 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 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 IA [auth D] SDF format, chain DA [auth C] SDF format, chain CA [auth C] 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 IA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] 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 IA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain CA [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 R [auth B] SDF format, chain QA [auth F] SDF format, chain PA [auth F] SDF format, chain KA [auth E] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain KA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain KA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	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 V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain S [auth B] SDF format, chain RA [auth F] SDF format, chain NA [auth E] 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 V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain NA [auth E] 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 V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain NA [auth E] 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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

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

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.592	α = 90
b = 137.81	β = 90
c = 223.165	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-22

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.