MolNFT v1 · #95012 · protein
Human atlastin-1 1-446, C-HIS6, GDPALF4-
4IDO: “Human atlastin-1 1-446, C-HIS6, GDPALF4-”. X-ray diffraction, 3 ligands (GDP, ALF, MG), 8 pockets (best druggability 0.87). MolNFT v1 #95012 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4IDO
- Type
- protein
- Length
- 834 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atlastin-1
- EC
- 3.6.5.-
- UniProt
- Q8WXF7
- Ligands
- GDP, ALF, MG
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atlastin-1 (EC 3.6.5.-) | protein | 412 | 47% helix, 17% strand | Q8WXF7 |
| B | Atlastin-1 (EC 3.6.5.-) | protein | 422 | 49% helix, 16% strand | Q8WXF7 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.87 | 0.94 | 81 | GDP, ALF, MG |
| 2 | 155 | 0.81 | 0.97 | 34 | empty |
| 3 | 313 | 0.70 | 0.84 | 34 | empty |
| 4 | 376 | 0.62 | 0.77 | 44 | empty |
| 5 | 399 | 0.60 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 3886 Ų buried · 26 hydrogen bonds · protein-protein
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 Q8WXF7
- Elsewhere: RCSB PDB 4IDO · PDBe 4IDO · UniProt Q8WXF7
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