Research workbench
Cryo-EM structure of human ABCA4 in the apo state
Analyse Cryo-EM structure of human ABCA4 in the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E7I
- Type
- protein
- Length
- 2,011 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal-specific phospholipid-transporting ATPase ABCA4
- EC
- 7.6.2.1
- UniProt
- P78363
- Ligands
- 3PE, NAG, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 43% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal-specific phospholipid-transporting ATPase ABCA4 (EC 7.6.2.1) | protein | 2011 | 43% helix, 7% strand | P78363 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.82 | 0.83 | 84 | empty |
| 2 | 982 | 0.79 | 0.81 | 86 | empty |
| 3 | 553 | 0.71 | 0.80 | 73 | empty |
| 4 | 161 | 0.66 | 0.86 | 22 | empty |
| 5 | 467 | 0.65 | 0.77 | 46 | empty |
Modifications
Observed in the structure: 9 glycan, 6 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 7E7I · Cryo-EM structure of human ABCA4 in the apo state · the same entry in another collection · chain A against A, TM-score 1.00
- P78363 · AlphaFold monomer V2.0 prediction for retinal-specific phospholipid- transporting ATPase… · 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 P78363
- Elsewhere: RCSB PDB 7E7I · PDBe 7E7I · UniProt P78363
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