1DPM

THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE WITH BOUND SUBSTRATE ANALOG DIETHYL 4-METHYLBENZYLPHOSPHONATE

Structural Biology Knowledgebase: 1DPM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.154

Literature

Macromolecules
Sequence Display for 1DPM

Classification: HYDROLASE

Total Structure Weight: 72752.85

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHOTRIESTERASE A, B 329 Brevundimonas diminuta EC#: 3.1.8.1 IUBMB
Gene Name(s): opd
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EBP
Query on EBP

A, B DIETHYL 4-METHYLBENZYLPHOSPHONATE
C12 H19 O3 P
QKGBKPZAXXBLJE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A, B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Observed:
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 129.60 α = 90.00
b = 91.40 β = 91.90
c = 69.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-02-13
  • Released Date: 1997-08-20
  • Deposition author(s): Vanhooke, J.L., Benning, M.M., Raushel, F.M., Holden, H.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4