Research workbench
Cryo-EM structure of human ABCA4 in nrpe-bound state
Analyse Cryo-EM structure of human ABCA4 in nrpe-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E7O
- Type
- protein
- Length
- 2,003 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, HZL, NAG, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 43% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal-specific phospholipid-transporting ATPase ABCA4 (EC 7.6.2.1) | protein | 2003 | 43% helix, 8% strand | P78363 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains A
- HZL · [(2S)-3-[2-[(E)-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenylidene]amino]ethoxy-oxidanyl-phosphoryl]oxy-2-[(Z)-octadec-9-enoyl]oxy-propyl] (Z)-octadec-9-enoate · ligand · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.82 | 0.83 | 94 | empty |
| 2 | 1061 | 0.81 | 0.82 | 109 | empty |
| 3 | 459 | 0.69 | 0.80 | 57 | empty |
| 4 | 494 | 0.67 | 0.78 | 45 | empty |
| 5 | 141 | 0.66 | 0.88 | 17 | empty |
Modifications
Observed in the structure: 9 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7E7O · Cryo-EM structure of human ABCA4 in NRPE-bound 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 0.94
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 7E7O · PDBe 7E7O · UniProt P78363
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