MolNFT v1 · #189796 · protein
Cryo-EM structure of human very long-chain fatty acid ABC transporter ABCD1
7VWC · Peroxisomal membrane protein RELATED,ATP-binding cassette…: “Cryo-EM structure of human very long-chain fatty acid ABC transporter ABCD1”. Electron microscopy, 1 ligand (82T), 13 pockets (best druggability 0.75). MolNFT v1 #189796…
- PDB
- 7VWC
- Type
- protein
- Length
- 1,229 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal membrane protein RELATED,ATP-binding cassette sub-family D member 1
- EC
- 7.6.2.-
- UniProt
- P33897
- Ligands
- 82T
- Pockets
- 13 · best druggability 0.75
Structure
electron microscopy · 2 distinct chains · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal membrane protein RELATED,ATP-binding cassette sub-family D member 1 (EC 7.6.2.-) | protein | 617 | 51% helix, 6% strand | P33897 |
| B | Peroxisomal membrane protein RELATED,ATP-binding cassette sub-family D member 1 (EC 7.6.2.-) | protein | 612 | 49% helix, 6% strand | P33897 |
Ligands and binding sites
- 82T · [(2R)-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-oxidanyl-propyl] octadecanoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.75 | 0.78 | 82 | 82T |
| 2 | 933 | 0.74 | 0.77 | 78 | empty |
| 3 | 239 | 0.53 | 0.76 | 42 | empty |
| 4 | 114 | 0.52 | 0.82 | 19 | empty |
| 5 | 251 | 0.51 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 7036 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 7VWC · Cryo-EM structure of human very long-chain fatty acid ABC transporter ABCD1 · the same entry in another collection · chain B against B, TM-score 1.00
- P33897 · AlphaFold monomer V2.0 prediction for ATP-binding cassette sub-family D member 1 (P33897) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 P33897
- Elsewhere: RCSB PDB 7VWC · PDBe 7VWC · UniProt P33897
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