6WK0

Crystal structure of human ribokinase in complex with AMPPCP and ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of human ribokinase

Park, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribokinase
A, B, C, D
317Homo sapiensMutation(s): 0 
Gene Names: RBKSRBSK
EC: 2.7.1.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H477 (Homo sapiens)
Explore Q9H477 
Go to UniProtKB:  Q9H477
PHAROS:  Q9H477
GTEx:  ENSG00000171174 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H477
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP (Subject of Investigation/LOI)
Query on ACP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
P [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
RIB (Subject of Investigation/LOI)
Query on RIB

Download Ideal Coordinates CCD File 
H [auth B],
L [auth C]
alpha-D-ribofuranose
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
J [auth B]
K [auth B]
N [auth C]
F [auth A],
G [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.02α = 90
b = 89.35β = 98.61
c = 144.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-04-21 
  • Deposition Author(s): Park, J.

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description