1GTV

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE-5'-DIPHOSPHATE (TDP)

Structural Biology Knowledgebase: 1GTV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 1GTV

Classification: TRANSFERASE

Total Structure Weight: 47029.04

Macromolecule Entities
Molecule Chains Length Organism Details
THYMIDYLATE KINASE A, B 214 Mycobacterium tuberculosis EC#: 2.7.4.9 IUBMB
Gene Name(s): tmk Rv3247c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TMP
Query on TMP

B THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TMP Ki: 4500 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.192
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 76.35 α = 90.00
b = 76.35 β = 90.00
c = 134.82 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-21
  • Released Date: 2002-03-28
  • Deposition author(s): Ursby, T., Weik, M., Fioravanti, E., Delarue, M., Goeldner, M., Bourgeois, D.

Revision History

  • 2013-08-07
    Type: Source and taxonomy | Details: SOURCE
  • 2013-08-07
    Type: Other | Details: REMARK 525
  • 2013-08-07
    Type: Refinement description | Details: REMARK 3
  • 2013-08-07
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2013-08-07
    Type: Version format compliance | Details: REMARK 4