5OCH

The crystal structure of human ABCB8 in an outward-facing state

PDB DOI: https://doi.org/10.2210/pdb5OCH/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2017-06-30 Released: 2018-07-25
Deposition Author(s): Faust, B., Pike, A.C.W., Shintre, C.A., Quiqley, A.M., Chu, A., Barr, A., Shrestha, L., Mukhopadhyay, S., Borkowska, O., Chalk, R., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Carpenter, E.P., Structural Genomics Consortium (SGC)
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.251 (Depositor), 0.260 (DCC)
R-Value Work:
0.231 (Depositor), 0.250 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of human ABCB8 in an outward-facing state

Faust, B., Pike, A.C.W., Shintre, C.A., Quiqley, A.M., Chu, A., Barr, A., Shrestha, L., Mukhopadhyay, S., Borkowska, O., Chalk, R., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Carpenter, E.P.

To be published.

Macromolecule Content

Total Structure Weight: 539.52 kDa
Atom Count: 31,278
Modelled Residue Count: 4,484
Deposited Residue Count: 4,896
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family B member 8, mitochondrial	A, C, D	612	Homo sapiens	Mutation(s): 0 Gene Names: ABCB8, MABC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUT2 (Homo sapiens) Explore Q9NUT2 Go to UniProtKB: Q9NUT2
PHAROS: Q9NUT2 GTEx: ENSG00000197150
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family B member 8, mitochondrial	B	612	Homo sapiens	Mutation(s): 0 Gene Names: ABCB8, MABC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUT2 (Homo sapiens) Explore Q9NUT2 Go to UniProtKB: Q9NUT2
PHAROS: Q9NUT2 GTEx: ENSG00000197150
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family B member 8, mitochondrial	E	612	Homo sapiens	Mutation(s): 0 Gene Names: ABCB8, MABC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUT2 (Homo sapiens) Explore Q9NUT2 Go to UniProtKB: Q9NUT2
PHAROS: Q9NUT2 GTEx: ENSG00000197150
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family B member 8, mitochondrial	F, G	612	Homo sapiens	Mutation(s): 0 Gene Names: ABCB8, MABC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUT2 (Homo sapiens) Explore Q9NUT2 Go to UniProtKB: Q9NUT2
PHAROS: Q9NUT2 GTEx: ENSG00000197150
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family B member 8, mitochondrial	H	612	Homo sapiens	Mutation(s): 0 Gene Names: ABCB8, MABC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUT2 (Homo sapiens) Explore Q9NUT2 Go to UniProtKB: Q9NUT2
PHAROS: Q9NUT2 GTEx: ENSG00000197150
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain EA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F]	BA [auth G] EA [auth H] K [auth A] N [auth B] S [auth D] BA [auth G], EA [auth H], K [auth A], N [auth B], S [auth D], V [auth E], Y [auth F]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G]	CA [auth H] I [auth A] L [auth B] O [auth C] Q [auth D] CA [auth H], I [auth A], L [auth B], O [auth C], Q [auth D], T [auth E], W [auth F], Z [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain CA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F]	AA [auth G] DA [auth H] J [auth A] M [auth B] P [auth C] AA [auth G], DA [auth H], J [auth A], M [auth B], P [auth C], R [auth D], U [auth E], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM Query on YCM	A, C, D	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.251 (Depositor), 0.260 (DCC)
R-Value Work: 0.231 (Depositor), 0.250 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.08	α = 90
b = 98.5	β = 90.5
c = 214.87	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-25

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2018-07-25
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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5OCH

The crystal structure of human ABCB8 in an outward-facing state

The crystal structure of human ABCB8 in an outward-facing state

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 4

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Entity ID: 5

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Experimental Data

Structure Validation

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Deposition Data

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