MolNFT v1 · #181668 · protein
Human ABCA4 structure in complex with N-ret-pe
7M1Q · Retinal-specific phospholipid-transporting ATPase ABCA4: “Human ABCA4 structure in complex with N-ret-pe”. Electron microscopy, 5 ligands (HZL, NAG, BMA), 20 pockets (best druggability 0.79). MolNFT v1 #181668 on GenesisL1: 3D…
- PDB
- 7M1Q
- Type
- protein
- Length
- 1,911 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
- HZL, NAG, BMA, MAN, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 48% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal-specific phospholipid-transporting ATPase ABCA4 (EC 7.6.2.1) | protein | 1911 | 48% helix, 6% strand | P78363 |
Ligands and binding sites
- 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 · 10 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- MG · Magnesium ion · metal · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.79 | 0.81 | 109 | MG |
| 2 | 448 | 0.77 | 0.85 | 76 | empty |
| 3 | 479 | 0.71 | 0.81 | 63 | empty |
| 4 | 359 | 0.68 | 0.82 | 52 | empty |
| 5 | 371 | 0.67 | 0.81 | 41 | empty |
Modifications
Observed in the structure: 8 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7M1Q · Human ABCA4 structure in complex with N-ret-PE · 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 7M1Q · PDBe 7M1Q · UniProt P78363
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