Structure of PDB 2d2g Chain A Binding Site BS03

Receptor Information

>2d2g Chain A (length=329) Species: 358 (Agrobacterium tumefaciens)

TGDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEK
AVRGLRHARAAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWF
DPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIKVATTGKATPFQEL
VLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSD
DTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGNASALALFGTRSWQTRAL
LIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRV
IPFLREKGVPPETLAGVTVANPARFLSPT

Ligand information

• Ligand ID: DZZ
• InChI: InChI=1S/C2H7O3PS/c1-4-6(3,7)5-2/h1-2H3,(H,3,7)
• InChIKey: WWJJVKAEQGGYHJ-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: COP(=S)(O)OC
  CACTVS 3.341: CO[P](O)(=S)OC
  ACDLabs 10.04: S=P(O)(OC)OC
• Formula: C2 H7 O3 P S
• Name: O,O-DIMETHYL HYDROGEN THIOPHOSPHATE;
  DIMETHYL THIOPHOSPHATE
• DrugBank: DB04687
• ZINC: ZINC000016039348
• PDB chain: 2d2g Chain A Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2d2g The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): H57 W131 K169 H201 R254 D301 F306
• Binding residue (residue number reindexed from 1): H25 W99 K137 H169 R222 D269 F274
• 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:2d2g, PDBe:2d2g, PDBj:2d2g
• PDBsum: 2d2g
• PubMed: 16054447
• UniProt: Q93LD7