6RUJ

Factor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)3-hydroxy-Leu peptide

PDB DOI: https://doi.org/10.2210/pdb6RUJ/pdb

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

Deposited: 2019-05-28 Released: 2020-07-08
Deposition Author(s): Nakashima, Y., McDonough, M.A., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.257
R-Value Work: 0.209
R-Value Observed: 0.211

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A human protein hydroxylase that accepts D-residues

Choi, H., Hardy, A., Leissing, T.M., Chowdhury, R., Ge, W., Markoulides, M., Scotti, J.S., Thorbjornsrud, H., Nakashima, Y., Kang, D., Hong, S., Lee, J., Park, H., McDonough, M.A., Schofield, C.J.

(2020) Commun Chem

DOI: https://doi.org/10.1038/s42004-020-0290-5

Macromolecule Content

Total Structure Weight: 42.45 kDa
Atom Count: 2,994
Modelled Residue Count: 364
Deposited Residue Count: 364
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(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 Gene Names: HIF1AN, FIH1 EC: 1.14.11.30 (PDB Primary Data), 1.14.11 (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-(D)3-hydroxy-Leu	B	15	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OGA (Subject of Investigation/LOI) Query on OGA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF 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] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [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] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF 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: 6RUJ	Ki: 1.20e+6 (nM) from 1 assay(s)
OGA	BindingDB: 6RUJ	IC50: 4.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.257
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.401	α = 90
b = 86.401	β = 90
c = 147.263	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Nakashima, Y.

McDonough, M.A.

Schofield, C.J.

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2024-01-24
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

6RUJ

Factor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)3-hydroxy-Leu peptide

A human protein hydroxylase that accepts D-residues

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2