1N5I

CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT PH 4.6 (RESOLUTION 1.85 A)

Structural Biology Knowledgebase: 1N5I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 1N5I

Classification: TRANSFERASE

Total Structure Weight: 23873.32

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

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

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TMP
Query on TMP

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

A CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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: 1.85 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.210
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.51 α = 90.00
b = 75.51 β = 90.00
c = 136.02 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-11-06
  • Released Date: 2003-04-08
  • Deposition author(s): Fioravanti, E., Haouz, A., Ursby, T., Munier-Lehmann, H., Delarue, M., Bourgeois, D.

Revision History

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