Structure of PDB 4np7 Chain A Binding Site BS03

Receptor Information

>4np7 Chain A (length=329) Species: 358 (Agrobacterium tumefaciens)

TGDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEK
AVRGLRHARAAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWF
DPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIKVATTGKATPFQEL
VLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSD
DTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGDASALALFGTRSWQTRAL
LIKALIDRGYKDRILVSHDWLFGFSLAVTNIMDVMDRINPDGMAFVPLRV
IPFLREKGVPPETLAGVTVANPARFLSPT

Ligand information

• Ligand ID: DPJ
• InChI: InChI=1S/C4H11O3PS/c1-3-6-8(5,9)7-4-2/h3-4H2,1-2H3,(H,5,9)
• InChIKey: PKUWKAXTAVNIJR-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCOP(=S)(O)OCC
  ACDLabs 10.04: S=P(O)(OCC)OCC
  CACTVS 3.341: CCO[P](O)(=S)OCC
• Formula: C4 H11 O3 P S
• Name: O,O-DIETHYL HYDROGEN THIOPHOSPHATE
• ChEMBL: CHEMBL1232328
• DrugBank: DB07674
• ZINC: ZINC000001565280
• PDB chain: 4np7 Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4np7 A 5000-fold increase in the specificity of a bacterial phosphotriesterase for malathion through combinatorial active site mutagenesis
• Resolution: 1.99 Å
• Binding residue (original residue number in PDB): H57 W131 K169 H201 H230 R254 Y257 D301
• Binding residue (residue number reindexed from 1): H25 W99 K137 H169 H198 R222 Y225 D269
• 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:4np7, PDBe:4np7, PDBj:4np7
• PDBsum: 4np7
• PubMed: 24721933
• UniProt: Q93LD7