4R1L

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution

PDB DOI: https://doi.org/10.2210/pdb4R1L/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: 2.42 Å
R-Value Free: 0.213
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a Hypothetical Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 206.5 kDa
Atom Count: 14,432
Modelled Residue Count: 1,714
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
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 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain H [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A]	BA [auth C], H [auth A]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain BA [auth C] Focus chain H [auth A] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain KA [auth D] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain U [auth B]	F [auth A], KA [auth D], U [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain KA [auth D] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain KA [auth D] Focus chain U [auth B]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain G [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain G [auth A]	AA [auth C], G [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain MA [auth D] MOL2 format, chain MA [auth D]	MA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain MA [auth D] Interactions & Density Focus chain MA [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain V [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain V [auth B]	EA [auth C] FA [auth C] M [auth A] N [auth A] NA [auth D] EA [auth C], FA [auth C], M [auth A], N [auth A], NA [auth D], O [auth A], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain V [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain JA [auth D] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C]	E [auth A], JA [auth D], T [auth B], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain JA [auth D] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain JA [auth D] Focus chain T [auth B] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	GA [auth C] HA [auth C] IA [auth C] OA [auth D] P [auth A] GA [auth C], HA [auth C], IA [auth C], OA [auth D], P [auth A], PA [auth D], Q [auth A], R [auth A], S [auth A], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain LA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D]	CA [auth C] DA [auth C] I [auth A] J [auth A] K [auth A] CA [auth C], DA [auth C], I [auth A], J [auth A], K [auth A], LA [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain LA [auth D] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain LA [auth D]