Research workbench
The crystal structure of human ABCB8 in an outward-facing state
Analyse The crystal structure of human ABCB8 in an outward-facing state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OCH
- Type
- protein
- Length
- 4,484 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-binding cassette sub-family B member 8, mitochondrial
- UniProt
- Q9NUT2
- Ligands
- ADP, Y01, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 63% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-binding cassette sub-family B member 8, mitochondrial | protein | 552 | 63% helix, 12% strand | Q9NUT2 |
| B | ATP-binding cassette sub-family B member 8, mitochondrial | protein | 573 | 64% helix, 11% strand | Q9NUT2 |
| C | ATP-binding cassette sub-family B member 8, mitochondrial | protein | 537 | 61% helix, 12% strand | Q9NUT2 |
| D | ATP-binding cassette sub-family B member 8, mitochondrial | protein | 573 | 64% helix, 11% strand | Q9NUT2 |
| E | ATP-binding cassette sub-family B member 8, mitochondrial | protein | 576 | 64% helix, 11% strand | Q9NUT2 |
| F | ATP-binding cassette sub-family B member 8, mitochondrial | protein | 573 | 64% helix, 11% strand | Q9NUT2 |
| G | ATP-binding cassette sub-family B member 8, mitochondrial | protein | 552 | 63% helix, 11% strand | Q9NUT2 |
| H | ATP-binding cassette sub-family B member 8, mitochondrial | protein | 548 | 62% helix, 11% strand | Q9NUT2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- Y01 · Cholesterol hemisuccinate · ligand · 7 copies · chains A, B, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.88 | 0.91 | 118 | empty |
| 2 | 1014 | 0.88 | 0.89 | 125 | Y01 |
| 3 | 1120 | 0.86 | 0.87 | 133 | Y01 |
| 4 | 1121 | 0.85 | 0.86 | 102 | empty |
| 5 | 1103 | 0.85 | 0.86 | 144 | Y01 |
Interfaces
9 interfaces between chains.
- A–B · 5998 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 5819 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 5226 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 5157 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 341 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (alkylation).
Compared structures
- 5OCH · The crystal structure of human ABCB8 in an outward-facing state · the same entry in another collection · chain H against H, TM-score 1.00
- Q9NUT2 · AlphaFold monomer V2.0 prediction for mitochondrial potassium channel ATP-binding subunit… · a predicted model of the same protein · chain C against A, TM-score 0.81
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9NUT2
- Elsewhere: RCSB PDB 5OCH · PDBe 5OCH · UniProt Q9NUT2
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