6YYX | pdb_00006yyx

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)

• PDB DOI: https://doi.org/10.2210/pdb6YYX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), synthetic construct
• Mutation(s): Yes 


• Deposited: 2020-05-06 Released: 2021-03-17 
• Deposition Author(s): Nakashima, Y., Brewitz, L., Schofield, C.J.

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Experimental Data Snapshot

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

Starting Model: experimental

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

• DOI: https://doi.org/10.1039/D0SC04301J

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: 53.81 kDa 
• Atom Count: 4,059 
• Modeled Residue Count: 447 
• 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): 0  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  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q1Z (Subject of Investigation/LOI)	D [auth A]	(3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid C6 H8 O5 BJQIUPTURRAODO-GSVOUGTGSA-N
MN (Subject of Investigation/LOI)	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.22	α = 90
b = 86.591	β = 90
c = 123.265	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Nakashima, Y., Brewitz, L., Schofield, C.J.

Revision History  

• 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