3UF0

Crystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from Beutenbergia cavernae(EFI target EFI-502044) with bound NADP (low occupancy)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from Beutenbergia cavernae(EFI target EFI-502044) with bound NADP (low occupancy)

Vetting, M.W., Toro, R., Bhosle, R., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short-chain dehydrogenase/reductase SDR
A, B
273Beutenbergia cavernae DSM 12333Mutation(s): 0 
Gene Names: Bcav_0642
EC: 1.1.1.125
UniProt
Find proteins for C5BY10 (Beutenbergia cavernae (strain ATCC BAA-8 / DSM 12333 / NBRC 16432))
Explore C5BY10 
Go to UniProtKB:  C5BY10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5BY10
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.47α = 90
b = 115.47β = 90
c = 76.182γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
MOSFLMdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description