4R1M

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.48 A resolution

PDB DOI: https://doi.org/10.2210/pdb4R1M/pdb

Classification: LIGASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-06 Released: 2014-08-27
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.200
R-Value Work: 0.175
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a Hypothetical Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.48 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 203.21 kDa
Atom Count: 13,860
Modelled Residue Count: 1,720
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylacetate-coenzyme A ligase	A, B, C, D	436	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_0428 EC: 6.2.1.30
UniProt
Find proteins for Q8AAN6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8AAN6 Go to UniProtKB: Q8AAN6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8AAN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain F [auth A] SDF format, chain R [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain R [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain R [auth B]	DA [auth D], F [auth A], R [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain DA [auth D] Focus chain F [auth A] Focus chain R [auth B] Interactions & Density Focus chain DA [auth D] Focus chain F [auth A] Focus chain R [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain E [auth A] SDF format, chain Q [auth B] SDF format, chain U [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C]	CA [auth D], E [auth A], Q [auth B], U [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain E [auth A] Focus chain Q [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain E [auth A] Focus chain Q [auth B] Focus chain U [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] EA [auth D] FA [auth D] H [auth A] AA [auth C], BA [auth C], EA [auth D], FA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], T [auth B], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] 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 T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] 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 T [auth B] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	X [auth C], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain X [auth C] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain G [auth A] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain G [auth A] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	G [auth A], S [auth B], V [auth C], W [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain G [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C]