5C41

Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers

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
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

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E [auth A],
H [auth B],
K [auth C],
N [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
PO4
Query on PO4

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O [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA
Query on NA

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F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
P [auth D],
Q [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.95α = 90
b = 89.19β = 98.16
c = 144.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata 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