1MCZ

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE

Structural Biology Knowledgebase: 1MCZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 1MCZ

Classification: LYASE

Total Structure Weight: 912260.25

Macromolecule Entities
Molecule Chains Length Organism Details
BENZOYLFORMATE DECARBOXYLASE A, B, C..., D, E, F, G, H, I, J, K, L, M, N, O, PA, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P 528 Pseudomonas putida EC#: 4.1.1.7 IUBMB
Gene Name(s): mdlC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RMN
Query on RMN

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P (R)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-SSDOTTSWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RMN N/A in BindingDB
N/A in BindingMoad
Ki: 1000000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.200
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 134.80 α = 90.00
b = 209.60 β = 97.10
c = 163.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-08-06
  • Released Date: 2003-02-25
  • Deposition author(s): Polovnikova, E.S., Bera, A.K., Hasson, M.S.

Revision History

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