3R6C

Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS179)

Structural Biology Knowledgebase: 3R6C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3R6C

Classification: Transferase / transferase inhibitor

Total Structure Weight: 79426.31

Macromolecule Entities
Molecule Chains Length Organism Details
Anthranilate phosphoribosyltransferase A, B 377 Mycobacterium tuberculosis EC#: 2.4.2.18 IUBMB
Gene Name(s): trpD Rv2192c MTCY190.03c

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PRP
Query on PRP

A, B ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
17N
Query on 17N

A, B 8-methoxyphenanthro[3,4-d][1,3]dioxole-5,6- dicarboxylic acid
C18 H12 O7
KTEBZKXXNMHJFH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
17N N/A in BindingDB
N/A in BindingMoad
Ki: 19000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.186
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.98 α = 90.00
b = 77.93 β = 110.18
c = 99.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-21
  • Released Date: 2012-09-26
  • Deposition author(s): Castell, A., Short, F.L., Lott, J.S., TB Structural Genomics Consortium (TBSGC)

Revision History

  • 2013-11-27
    Type: Citation | Details: Citation update
  • 2013-04-10
    Type: Citation | Details: Citation update
  • 2013-02-20
    Type: Citation | Details: Citation update