Research workbench
Cryo-EM structure of the human ABCB6 (coproporphyrin III-bound)
Analyse Cryo-EM structure of the human ABCB6 (coproporphyrin III-bound) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DNY
- Type
- protein
- Length
- 1,146 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, HT9
- Pockets
- 16 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 65% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-binding cassette sub-family B member 6, mitochondrial | protein | 571 | 65% helix, 9% strand | Q9NP58 |
| B | ATP-binding cassette sub-family B member 6, mitochondrial | protein | 575 | 65% helix, 5% strand | Q9NP58 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 5 copies · chains A, B
- HT9 · coproporphyrin III · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.81 | 0.83 | 86 | empty |
| 2 | 158 | 0.75 | 0.92 | 33 | empty |
| 3 | 521 | 0.71 | 0.80 | 54 | empty |
| 4 | 64 | 0.70 | 0.96 | 21 | empty |
| 5 | 156 | 0.63 | 0.85 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 5402 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7DNY · Cryo-EM structure of the human ABCB6 (coproporphyrin III-bound) · the same entry in another collection · chain B against B, 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 0.90
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 7DNY · PDBe 7DNY · UniProt Q9NP58
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