4L8K | pdb_00004l8k

Crystal structure of a putative peptidase (PARMER_02772) from Parabacteroides merdae ATCC 43184 at 2.26 A resolution

PDB DOI: https://doi.org/10.2210/pdb4L8K/pdb

Classification: HYDROLASE
Organism(s): Parabacteroides merdae ATCC 43184
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-17 Released: 2013-07-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.159 (Depositor), 0.160 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative peptidase (PARMER_02772) from Parabacteroides merdae ATCC 43184 at 2.26 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 150.08 kDa
Atom Count: 10,840
Modeled Residue Count: 1,246
Deposited Residue Count: 1,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative peptidase	A, B, C, D	320	Parabacteroides merdae ATCC 43184	Mutation(s): 0 Gene Names: PARMER_02772, ZP_02032754.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] K [auth B] L [auth B] Q [auth C] F [auth A], G [auth A], K [auth B], L [auth B], Q [auth C], W [auth D], X [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D] Focus chain X [auth D]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B]	M [auth B], R [auth C], S [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A] I [auth B] J [auth B] N [auth C] O [auth C] E [auth A], I [auth B], J [auth B], N [auth C], O [auth C], P [auth C], U [auth D], V [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain H [auth A] MOL2 format, chain T [auth C] MOL2 format, chain H [auth A] mmCIF format, chain T [auth C] mmCIF format, chain H [auth A]	H [auth A], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain T [auth C] Interactions & Density Focus chain H [auth A] Focus chain T [auth C]