1OGD

The Structure of Bacillus subtilis RbsD complexed with D-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 1OGD

Classification: TRANSPORT

Total Structure Weight: 72043.74

Macromolecule Entities
Molecule Chains Length Organism Details
HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD A, B, C, D, E 131 Bacillus subtilis EC#: 5.4.99.62 IUBMB
Details: D-RIBOSE
Gene Name(s): rbsD BSU35930
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E RIBOSE(PYRANOSE FORM)
C5 H10 O5
SRBFZHDQGSBBOR-TXICZTDVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RIP N/A in BindingDB
Kd: 930000 nM  BindingMOAD
Kd: 930000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.198
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 123.51 α = 90.00
b = 108.66 β = 128.68
c = 83.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-30
  • Released Date: 2003-09-01
  • Deposition author(s): Kim, M.-S., Oh, B.-H.

Revision History

  • Version 1_0: 2003-09-01

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance