3D7K

Crystal structure of benzaldehyde lyase in complex with the inhibitor MBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 3D7K

Classification: LYASE

Total Structure Weight: 121087.15

Macromolecule Entities
Molecule Chains Length Organism Details
Benzaldehyde lyase A, B 570 Pseudomonas fluorescens EC#: 4.1.2.38 IUBMB
Gene Name(s): bznB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
D7K
Query on D7K

A, B 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]- 2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}- 5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)- 4-methyl-1,3-thiazol-3-ium
C20 H28 N4 O11 P3 S
NEEQBMRCDKRNBV-FQEVSTJZSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
D7K N/A in BindingDB
N/A in BindingMoad
Kd: 25000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.194
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 151.94 α = 90.00
b = 151.94 β = 90.00
c = 98.22 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-05-21
  • Released Date: 2008-07-01
  • Deposition author(s): Brandt, G.S.

Revision History

  • Version 1_0: 2008-07-01

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance