Structure of PDB 1dpm Chain B

Receptor sequence

>1dpmB (length=329) Species: 293 (Brevundimonas diminuta)

ARINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAV
RGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDP
PLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVL
KAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDT
DDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLI
KALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIP
FLREKGVPQETLAGITVTNPARFLSPTLR

3D structure

• PDB: 1dpm Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate.
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H55 H57 K169 H201 H230 D233 H254 D301
• Catalytic site (residue number reindexed from 1): H21 H23 K135 H167 H196 D199 H220 D267
• Enzyme Commision number: 3.1.8.1: aryldialkylphosphatase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	B	H55 H57 D301	H21 H23 D267
BS02	ZN	B	H201 H230	H167 H196
BS03	EBP	B	W131 H201 H257 L271 D301 M317	W97 H167 H223 L237 D267 M283
BS04	EBP	B	Q155 Y156	Q121 Y122

Gene Ontology

Molecular Function

• GO:0004063 aryldialkylphosphatase activity
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0046872 metal ion binding

Biological Process

• GO:0009056 catabolic process

Cellular Component

• GO:0005886 plasma membrane

External links

• PDB: RCSB:1dpm, PDBe:1dpm, PDBj:1dpm
• PDBsum: 1dpm
• PubMed: 8634243
• UniProt: P0A434|OPD_BREDI Parathion hydrolase (Gene Name=opd)