4B7E

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

PDB DOI: https://doi.org/10.2210/pdb4B7E/pdb

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

Deposited: 2012-08-17 Released: 2013-01-23
Deposition Author(s): Chowdhury, R., Ge, W., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.255
R-Value Work: 0.226
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/anie.201208046
Primary Citation of Related Structures:
4B7E, 4B7K

Organizational Affiliation

Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK.

Macromolecule Content

Total Structure Weight: 43.24 kDa
Atom Count: 3,173
Modelled Residue Count: 366
Deposited Residue Count: 366
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NWT6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CONSENSUS ANKYRIN REPEAT DOMAIN-LEU	B	17	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OGA Query on OGA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	N-OXALYLGLYCINE C₄ H₅ N O₅ BIMZLRFONYSTPT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	J [auth A], K [auth A], L [auth A], M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
OGA	BindingDB: 4B7E	Ki: 1.20e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.255
R-Value Work: 0.226
R-Value Observed: 0.226
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.448	α = 90
b = 86.448	β = 90
c = 143.958	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-01-23

Deposition Author(s):

Chowdhury, R.

Ge, W.

Schofield, C.J.

Revision History (Full details and data files)

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

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Help and Resources

4B7E

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

Substrate selectivity analyses of factor inhibiting hypoxia-inducible factor.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2