7BMI | pdb_00007bmi

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

• PDB DOI: https://doi.org/10.2210/pdb7BMI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-20 Released: 2021-06-02 
• Deposition Author(s): Nakashima, Y., Brewitz, L., Schofield, C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Fluorinated derivatives of pyridine-2,4-dicarboxylate are potent inhibitors of human 2-oxoglutarate dependent oxygenases

Brewitz, L., Nakashima, Y., Tumber, A., Salah, E., Schofield, C.J.

(2021) J Fluor Chem 247: 109804

• DOI: https://doi.org/10.1016/j.jfluchem.2021.109804

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: 53.84 kDa 
• Atom Count: 4,009 
• 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): 0  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
U4B (Subject of Investigation/LOI)	D [auth A]	3-fluoranylpyridine-2,4-dicarboxylic acid C7 H4 F N O4 IEQUQLPYQQVCNF-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
U4B	BindingDB:  7BMI	IC50: 110 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.702	α = 90
b = 91.274	β = 90
c = 122.629	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Nakashima, Y., Brewitz, L., Schofield, C.J.

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary