4BUC

CRYSTAL STRUCTURE OF MURD LIGASE FROM THERMOTOGA MARITIMA IN APO FORM

Structural Biology Knowledgebase: 4BUC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.163

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4BUC

Classification: LIGASE

Total Structure Weight: 106575.94

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE A, B 450 Thermotoga maritima EC#: 6.3.2.9 IUBMB
Gene Name(s): murD TM_0234
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO3
Query on PO3

A, B PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NH4
Query on NH4

A, B AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.163
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.17 α = 90.00
b = 135.85 β = 98.17
c = 67.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-20
  • Released Date: 2013-07-17
  • Deposition author(s): Favini-Stabile, S., Contreras-Martel, C., Thielens, N., Dessen, A.

Revision History

  • 2013-12-18
    Type: Citation | Details: JRNL