2FV7

Crystal structure of human ribokinase

Structural Biology Knowledgebase: 2FV7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2FV7

Classification: TRANSFERASE

Total Structure Weight: 71241.38

Macromolecule Entities
Molecule Chains Length Organism Details
Ribokinase A, B 331 Homo sapiens EC#: 2.7.1.15 IUBMB
Gene Name(s): RBKS Gene View RBSK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A, B UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.198
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 45.53 α = 90.00
b = 72.98 β = 91.08
c = 90.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-01-30
  • Released Date: 2006-02-28
  • Deposition author(s): Rabeh, W.M., Tempel, W., Nedyalkova, L., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values