Research workbench
Cryo-EM structure of ATP-bound human very long-chain fatty acid ABC transporter ABCD1
Analyse Cryo-EM structure of ATP-bound human very long-chain fatty acid ABC transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VX8
- Type
- protein
- Length
- 1,120 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
- 3.1.2.-, 7.6.2.-
- UniProt
- P33897
- Ligands
- ATP, MG
- Pockets
- 14 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Peroxisomal membrane protein RELATED,ATP-binding cassette sub-family D member 1 (EC 3.1.2.-, 7.6.2.-) | protein | 560 | 58% helix, 8% strand | P33897 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.87 | 0.89 | 142 | ATP, MG |
| 2 | 1190 | 0.72 | 0.76 | 91 | empty |
| 3 | 556 | 0.66 | 0.77 | 58 | empty |
| 4 | 493 | 0.64 | 0.76 | 49 | empty |
| 5 | 258 | 0.54 | 0.76 | 45 | empty |
Interfaces
1 interface between chains.
- B–A · 6378 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 7VX8 · Cryo-EM structure of ATP-bound 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 0.92
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 7VX8 · PDBe 7VX8 · UniProt P33897
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.