4XDA

Vibrio cholerae O395 Ribokinase complexed with Ribose, ADP and Sodium ion.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of Apo and Ligand Bound Vibrio cholerae Ribokinase (Vc-RK): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation

Paul, R.Patra, M.D.Sen, U.

(2015) Adv.Exp.Med.Biol. 842: 293-307


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribokinase
A, B, C, D
309Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)Mutation(s): 0 
Gene Names: rbsK
EC: 2.7.1.15
Find proteins for A0A0H2UL04 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Go to UniProtKB:  A0A0H2UL04
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
RIB
Query on RIB

Download SDF File 
Download CCD File 
A, C, D
RIBOSE
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 59.420α = 106.29
b = 70.700β = 97.65
c = 79.880γ = 98.68
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology, Department of Atomic EnergyIndiaMSACR project

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release