5C3Y

Structure of human ribokinase crystallized with AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of human ribokinase crystallized with AMPPNP

Park, J.Chakrabarti, J.Singh, B.Gupta, R.S.Junop, M.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribokinase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
330Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AN2
Query on AN2

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
HA [auth H]
KA [auth I]
M [auth A]
BA [auth F],
EA [auth G],
HA [auth H],
KA [auth I],
M [auth A],
NA [auth J],
P [auth B],
QA [auth K],
S [auth C],
TA [auth L],
V [auth D],
Y [auth E]
AMP PHOSPHORAMIDATE
C10 H16 N6 O9 P2
FQMDCEJHLOLKLI-KQYNXXCUSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
DA [auth F]
FA [auth G]
GA [auth G]
AA [auth E],
CA [auth F],
DA [auth F],
FA [auth G],
GA [auth G],
IA [auth H],
JA [auth H],
LA [auth I],
MA [auth I],
N [auth A],
O [auth A],
OA [auth J],
PA [auth J],
Q [auth B],
R [auth B],
RA [auth K],
SA [auth K],
T [auth C],
U [auth C],
UA [auth L],
VA [auth L],
W [auth D],
X [auth D],
Z [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.31α = 90
b = 168.14β = 90.82
c = 161.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references, Structure summary
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description