Research workbench
Cryo-EM structure of human lysosomal cobalamin exporter ABCD4
Analyse Cryo-EM structure of human lysosomal cobalamin exporter ABCD4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JBJ
- Type
- protein
- Length
- 1,130 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-binding cassette sub-family D member 4
- UniProt
- O14678
- Ligands
- ATP
- Pockets
- 11 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-binding cassette sub-family D member 4 | protein | 565 | 57% helix, 4% strand | O14678 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.84 | 0.94 | 35 | empty |
| 2 | 918 | 0.79 | 0.81 | 67 | empty |
| 3 | 675 | 0.78 | 0.83 | 80 | ATP |
| 4 | 674 | 0.77 | 0.82 | 85 | ATP |
| 5 | 181 | 0.48 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 8251 Ų buried · 105 hydrogen bonds · protein-protein
Compared structures
- 6JBJ · Cryo-EM structure of human lysosomal cobalamin exporter ABCD4 · the same entry in another collection · chain A against A, TM-score 1.00
- O14678 · AlphaFold monomer V2.0 prediction for lysosomal cobalamin transporter ABCD4 (O14678) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O14678
- Elsewhere: RCSB PDB 6JBJ · PDBe 6JBJ · UniProt O14678
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