6Q9F

Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Mn, NOG and Factor X peptide fragment (39mer-4Ser)

• PDB DOI: https://doi.org/10.2210/pdb6Q9F/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-12-18 Released: 2020-01-15 
• Deposition Author(s): Chowdhury, R., Pfeffer, I., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.200 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Mn, NOG and Factor X peptide fragment (39mer-4Ser)

Pfeffer, I., Chowdhury, R., Schofield, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 54.01 kDa 
• Atom Count: 4,186 
• Modelled Residue Count: 449 
• Deposited Residue Count: 468 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartyl/asparaginyl beta-hydroxylase	A	429	Homo sapiens	Mutation(s): 1  Gene Names: ASPH, BAH 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	B	39	Homo sapiens	Mutation(s): 4  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA	D [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.200 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.808	α = 90
b = 91.541	β = 90
c = 122.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Chowdhury, R., Pfeffer, I., Schofield, C.J.

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary