8D3O

Crystal structure of human Apoptosis-Inducing Factor (AIF) complexed with 8-methoxyquinolin-4-amine

PDB DOI: https://doi.org/10.2210/pdb8D3O/pdb

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

Deposited: 2022-06-01 Released: 2023-11-08
Deposition Author(s): Brosey, C.A., Tainer, J.A.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.237
R-Value Work: 0.213
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Integrating early structural selection into chemical library screening for drug discovery with high-throughput small-angle X-ray scattering (SAXS)

Brosey, C.A., Link, T., Shen, R., Moiani, D., Burnett, K., Hura, G., Jones, D.E., Tainer, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 122.3 kDa
Atom Count: 6,828
Modelled Residue Count: 880
Deposited Residue Count: 1,093
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis-inducing factor 1, mitochondrial	A, B	543	Homo sapiens	Mutation(s): 0 Gene Names: AIFM1, AIF, PDCD8 EC: 1.6.99
UniProt & NIH Common Fund Data Resources
Find proteins for O95831 (Homo sapiens) Explore O95831 Go to UniProtKB: O95831
PHAROS: O95831 GTEx: ENSG00000156709
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95831
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis-inducing factor (AIF), unidentified helix	C [auth D]	7	Homo sapiens	Mutation(s): 0 Gene Names: AIFM1 EC: 1.6.99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B]	F [auth A], K [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
QF6 (Subject of Investigation/LOI) Query on QF6 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B]	D [auth A], J [auth B]	8-methoxyquinolin-4-amine C₁₀ H₁₀ N₂ O QMBPJEIUEYDRGP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	G [auth A] H [auth A] I [auth A] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.237
R-Value Work: 0.213
R-Value Observed: 0.214
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.104	α = 90
b = 115.045	β = 90
c = 122.167	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-08

Deposition Author(s):

Brosey, C.A.

Tainer, J.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 CA220430
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA092584
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP180813

Revision History (Full details and data files)

Version 1.0: 2023-11-08
Type: Initial release

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Help and Resources

8D3O

Crystal structure of human Apoptosis-Inducing Factor (AIF) complexed with 8-methoxyquinolin-4-amine

Integrating early structural selection into chemical library screening for drug discovery with high-throughput small-angle X-ray scattering (SAXS)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2