Research workbench
Cryo-EM structure of C22:0-CoA bound human very long-chain fatty acid ABC transporter ABCD1
Analyse Cryo-EM structure of C22:0-CoA bound human very long-chain fatty acid ABC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VZB
- Type
- protein
- Length
- 1,170 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
- Y01, FFI
- Pockets
- 16 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 58% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisomal membrane protein RELATED,ATP-binding cassette sub-family D member 1 (EC 3.1.2.-, 7.6.2.-) | protein | 585 | 58% helix, 7% strand | P33897 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains A, B
- FFI · S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] docosanethioate · ligand · 2 copies · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.78 | 0.81 | 86 | FFI |
| 2 | 836 | 0.78 | 0.81 | 81 | FFI |
| 3 | 160 | 0.73 | 0.90 | 36 | empty |
| 4 | 142 | 0.72 | 0.91 | 31 | empty |
| 5 | 88 | 0.65 | 0.90 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 5700 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 7VZB · Cryo-EM structure of C22:0-CoA bound human very long-chain fatty acid ABC transporter… · the same entry in another collection · chain A against A, 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 0.91
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 7VZB · PDBe 7VZB · UniProt P33897
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