6YYX

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-methyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q1ZClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Synthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human aspartate/asparagine-beta-hydroxylase

Brewitz, L.Nakashima, Y.Schofield, C.J.

(2021) Chem Sci 12: 1327-1342


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartyl/asparaginyl beta-hydroxylase429Homo sapiensMutation(s): 0 
Gene Names: ASPHBAH
EC: 1.14.11.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q12797 (Homo sapiens)
Explore Q12797 
Go to UniProtKB:  Q12797
PHAROS:  Q12797
GTEx:  ENSG00000198363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12797
Sequence Annotations
Expand
  • Reference Sequence
6YYX_1
050100150200250300350400
6YYX_1
UNIPROT Q12797
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor X39Homo sapiensMutation(s): 4 
Gene Names: F10
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
6YYX_2
0510152025303540
6YYX_2
DGDQSETSPSQNQGKCKDGLGEYTCTSLEGFEGKNSELF
UNIPROT P00742
DGDQCETSPCQNQGKCKDGLGEYTCTCLEGFEGKNCELF
UNMODELED
MUTATION
HYDROPATHY
DISORDER
DISORDERED BINDING
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.22α = 90
b = 86.591β = 90
c = 123.265γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q1ZClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary