3I3Y

Crystal structure of Ribokinase in Complex with D-Ribose from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbohydrate kinase
A, B, C, D
299Klebsiella pneumoniae subsp. pneumoniae MGH 78578Mutation(s): 0 
Gene Names: 5340552KPN78578_16990KPN_01729
EC: 2.7.1.15
UniProt
Find proteins for A6T989 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6T989 
Go to UniProtKB:  A6T989
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6T989
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RIB
Query on RIB

Download Ideal Coordinates CCD File 
L [auth D]alpha-D-ribofuranose
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
SO4
Query on SO4

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E [auth B]
F [auth B]
G [auth B]
H [auth C]
I [auth C]
E [auth B],
F [auth B],
G [auth B],
H [auth C],
I [auth C],
K [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.488α = 90
b = 105.9β = 99.45
c = 121.152γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNSrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-02-10
    Changes: Database references, Structure summary