Structure of PDB 2d2j Chain A Binding Site BS03

Receptor Information

>2d2j Chain A (length=329) Species: 358 (Agrobacterium tumefaciens)

TGDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEK
AVRGLRHARAAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWF
DPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIKVATTGKATPFQEL
VLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSD
DTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGNASALALFGTRSWQTRAL
LIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRV
IPFLREKGVPPETLAGVTVANPARFLSPT

Ligand information

• Ligand ID: EDO
• InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
• InChIKey: LYCAIKOWRPUZTN-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341: OCCO
  OpenEye OEToolkits 1.5.0: C(CO)O
• Formula: C2 H6 O2
• Name: 1,2-ETHANEDIOL;
  ETHYLENE GLYCOL
• ChEMBL: CHEMBL457299
• ZINC: ZINC000005224354
• PDB chain: 2d2j Chain A Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2d2j The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): H57 W131
• Binding residue (residue number reindexed from 1): H25 W99
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H55 H57 K169 H201 H230 D233 R254 D301
• Catalytic site (residue number reindexed from 1): H23 H25 K137 H169 H198 D201 R222 D269
• Enzyme Commision number: 3.1.8.1: aryldialkylphosphatase.

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0046872 metal ion binding

Biological Process

• GO:0009056 catabolic process

External links

• PDB: RCSB:2d2j, PDBe:2d2j, PDBj:2d2j
• PDBsum: 2d2j
• PubMed: 16054447
• UniProt: Q93LD7