4B7K | pdb_00004b7k

FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH CONSENSUS ANKYRIN REPEAT DOMAIN-SER PEPTIDE (20-MER)

• PDB DOI: https://doi.org/10.2210/pdb4B7K/pdb

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


• Deposited: 2012-08-20 Released: 2013-01-23 
• Deposition Author(s): Chowdhury, R., Ge, W., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Substrate selectivity analyses of factor inhibiting hypoxia-inducible factor.

Yang, M., Hardy, A.P., Chowdhury, R., Loik, N.D., Scotti, J.S., McCullagh, J.S., Claridge, T.D., McDonough, M.A., Ge, W., Schofield, C.J.

(2013) Angew Chem Int Ed Engl 52: 1700-1704

• PubMed: 23296631 
• DOI: https://doi.org/10.1002/anie.201208046
• Primary Citation Related Structures: 
  4B7E, 4B7K

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Organizational Affiliation: 
• Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 43.13 kDa 
• Atom Count: 2,957 
• Modeled Residue Count: 353 
• Deposited Residue Count: 369 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR	A	349	Homo sapiens	Mutation(s): 0  EC: 1.14.11.16 (PDB Primary Data), 1.14.11.30 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens) Explore Q9NWT6  Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6 GTEx:  ENSG00000166135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CONSENSUS ANKYRIN REPEAT DOMAIN-SER	B	20	synthetic construct	Mutation(s): 0

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
SO4	E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OGA	BindingDB:  4B7K	Ki: 1.20e+6 (nM) from 1 assay(s)
		IC50: 4.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.355	α = 90
b = 86.355	β = 90
c = 148.308	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Chowdhury, R., Ge, W., Schofield, C.J.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2018-03-28
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description