2OLC

Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho

Structural Biology Knowledgebase: 2OLC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2OLC

Classification: Transferase

Total Structure Weight: 92410.03

Macromolecule Entities
Molecule Chains Length Organism Details
Methylthioribose kinase A, B 397 Bacillus subtilis EC#: 2.7.1.100 IUBMB
Gene Name(s): mtnK ykrT BSU13560
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- PROPANESULFONATE
CHAPS (Synonym)
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADP
Query on ADP

A, B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HO
Query on HO

A, B HOLMIUM ATOM
Ho
KJZYNXUDTRRSPN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.214
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 215.20 α = 90.00
b = 83.60 β = 90.00
c = 51.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-01-18
  • Released Date: 2007-05-22
  • Deposition author(s): Ku, S.Y., Smith, G.D., Howell, P.L.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4