MolNFT v1 · #181120 · protein
Structure of ATP-bound human ABCA4
7LKZ · Retinal-specific phospholipid-transporting ATPase ABCA4: “Structure of ATP-bound human ABCA4”. Electron microscopy, 6 ligands (POV, 6OU, ATP), 20 pockets (best druggability 0.85). MolNFT v1 #181120 on GenesisL1: 3D structure…
- PDB
- 7LKZ
- Type
- protein
- Length
- 1,920 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
- POV, 6OU, ATP, NAG, BMA, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal-specific phospholipid-transporting ATPase ABCA4 (EC 7.6.2.1) | protein | 1920 | 50% helix, 10% strand | P78363 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 5 copies · chains A
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 3 copies · chains A
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MG · Magnesium ion · metal · 2 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.85 | 0.90 | 54 | empty |
| 2 | 925 | 0.83 | 0.84 | 89 | 6OU |
| 3 | 704 | 0.82 | 0.86 | 85 | MG, ATP |
| 4 | 391 | 0.80 | 0.89 | 36 | empty |
| 5 | 410 | 0.73 | 0.83 | 46 | empty |
Modifications
Observed in the structure: 10 glycan, 6 disulfide, 2 covalent (N-glycosylation, disulfide, covalent ligand, glycosylation).
Compared structures
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 7LKZ · PDBe 7LKZ · UniProt P78363
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