1RKD

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP

Structural Biology Knowledgebase: 1RKD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1RKD

Classification: CARBOHYDRATE KINASE

Total Structure Weight: 33087.93

Macromolecule Entities
Molecule Chains Length Organism Details
RIBOKINASE A 309 Escherichia coli EC#: 2.7.1.15 IUBMB
Gene Name(s): rbsK b3752 JW3731
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

A RIBOSE
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.220
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 95.40 α = 90.00
b = 95.40 β = 90.00
c = 154.87 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-11-29
  • Released Date: 1998-03-04
  • Deposition author(s): Sigrell, J.A., Cameron, A.D., Jones, T.A., Mowbray, S.L.

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values