1MD9

CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB AND AMP

Structural Biology Knowledgebase: 1MD9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.232

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1MD9

Classification: LIGASE

Total Structure Weight: 60865.35

Macromolecule Entities
Molecule Chains Length Organism Details
2,3-dihydroxybenzoate-AMP ligase A 539 Bacillus subtilis EC#: 6.3.2 IUBMB
Gene Name(s): dhbE entE BSU31980

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

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DBH
Query on DBH

A 2,3-DIHYDROXY-BENZOIC ACID
C7 H6 O4
GLDQAMYCGOIJDV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.232
  • Space Group: P 31

Unit Cell:

Length (Å) Angle (°)
a = 66.90 α = 90.00
b = 66.90 β = 90.00
c = 114.80 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-08-07
  • Released Date: 2002-09-11
  • Deposition author(s): May, J.J., Kessler, N., Marahiel, M.A., Stubbs, M.T.

Revision History

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