Research workbench
Human ATL1 GTPase domain bound to GDP
Analyse Human ATL1 GTPase domain bound to GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B9G
- Type
- protein
- Length
- 1,221 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atlastin-1
- EC
- 3.6.5.-
- UniProt
- Q8WXF7
- Ligands
- GDP, MG
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Atlastin-1 (EC 3.6.5.-) | protein | 305 | 38% helix, 22% strand | Q8WXF7 |
| C | Atlastin-1 (EC 3.6.5.-) | protein | 306 | 38% helix, 22% strand | Q8WXF7 |
| D, A | Atlastin-1 (EC 3.6.5.-) | protein | 305 | 37% helix, 22% strand | Q8WXF7 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains B, C, D, A
- MG · Magnesium ion · metal · 4 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.88 | 0.89 | 100 | GDP, MG |
| 2 | 1065 | 0.88 | 0.89 | 100 | GDP, MG |
| 3 | 1083 | 0.74 | 0.77 | 78 | empty |
| 4 | 60 | 0.32 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1274 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1252 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 435 Ų buried · 3 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 6B9G · PDBe 6B9G · UniProt Q8WXF7
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