Structure of PDB 3wpm Chain A Binding Site BS02

Receptor Information

>3wpm Chain A (length=408) Species: 627192 (Sphingobium sp. SYK-6)

AKIIGGFAVSHTPTIAFAHDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVY
NDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAEC
LVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPI
PKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEW
DMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKT
LHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEG
TYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKS
LIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTR
NAAITYSV

Ligand information

• Ligand ID: GDE
• InChI: InChI=1S/C7H6O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1-2,8-10H,(H,11,12)
• InChIKey: LNTHITQWFMADLM-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.2: c1c(cc(c(c1O)O)O)C(=O)O
  CACTVS 3.370: OC(=O)c1cc(O)c(O)c(O)c1
  ACDLabs 12.01: O=C(O)c1cc(O)c(O)c(O)c1
• Formula: C7 H6 O5
• Name: 3,4,5-trihydroxybenzoic acid;
  Gallate
• ChEMBL: CHEMBL288114
• ZINC: ZINC000000001504
• PDB chain: 3wpm Chain B Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3wpm Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): E377 Y412
• Binding residue (residue number reindexed from 1): E371 Y406
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H12 H59 H192 E239
• Catalytic site (residue number reindexed from 1): H11 H53 H186 E233
• Enzyme Commision number: 1.13.11.-

Gene Ontology

Molecular Function

• GO:0008198 ferrous iron binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

External links

• PDB: RCSB:3wpm, PDBe:3wpm, PDBj:3wpm
• PDBsum: 3wpm
• PubMed: 24657997
• UniProt: G2IKE5