5OCH | pdb_00005och

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 OPM PDBTM MemProtMD

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), 0.263 (DCC)
R-Value Work:
0.231 (Depositor), 0.248 (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
Modeled Residue Count: 4,484
Deposited Residue Count: 4,896
Unique protein chains: 5

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Y [auth F] SDF format, chain V [auth E] SDF format, chain EA [auth H] SDF format, chain BA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain EA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain EA [auth H] mmCIF format, chain BA [auth G]	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 I [auth A] SDF format, chain Q [auth D] SDF format, chain W [auth F] SDF format, chain Z [auth G] SDF format, chain T [auth E] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain CA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain T [auth E] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain CA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain T [auth E] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain CA [auth H]	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 M [auth B] SDF format, chain P [auth C] SDF format, chain U [auth E] SDF format, chain X [auth F] SDF format, chain R [auth D] SDF format, chain J [auth A] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] MOL2 format, chain R [auth D] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F] mmCIF format, chain R [auth D] mmCIF format, chain J [auth A]	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), 0.263 (DCC)
R-Value Work: 0.231 (Depositor), 0.248 (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

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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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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

5OCH | pdb_00005och

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

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

Expand

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

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)