MolNFT v1 · #176477 · protein
Cryo-EM structure of the human ABCB6 (hemin and gsh-bound)
7DNZ · ATP-binding cassette sub-family B member 6, mitochondrial: “Cryo-EM structure of the human ABCB6 (hemin and gsh-bound)”. Electron microscopy, 3 ligands (Y01, GSH, HEM), 19 pockets (best druggability 0.82). MolNFT v1 #176477 on…
- PDB
- 7DNZ
- Type
- protein
- Length
- 1,182 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-binding cassette sub-family B member 6, mitochondrial
- UniProt
- Q9NP58
- Ligands
- Y01, GSH, HEM
- Pockets
- 19 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 64% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-binding cassette sub-family B member 6, mitochondrial | protein | 591 | 64% helix, 8% strand | Q9NP58 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 6 copies · chains A, B
- GSH · Glutathione · ligand · 4 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.82 | 0.83 | 107 | GSH |
| 2 | 604 | 0.70 | 0.79 | 56 | GSH |
| 3 | 165 | 0.69 | 0.88 | 30 | empty |
| 4 | 242 | 0.65 | 0.83 | 27 | GSH |
| 5 | 170 | 0.62 | 0.84 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 5697 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7DNZ · Cryo-EM structure of the human ABCB6 (Hemin and GSH-bound) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NP58 · AlphaFold monomer V2.0 prediction for ATP-binding cassette sub-family B member 6… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9NP58
- Elsewhere: RCSB PDB 7DNZ · PDBe 7DNZ · UniProt Q9NP58
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