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
R-Value Work: 0.231
R-Value Observed: 0.232

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

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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

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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

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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

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(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

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 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] SDF format, chain BA [auth G] SDF 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] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H]	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]	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]	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
R-Value Work: 0.231
R-Value Observed: 0.232
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

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Help and Resources

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

Sequence Annotations

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt & NIH Common Fund Data Resources

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)