Research workbench
Dynamin 1 GTPase dimer, short axis form
Analyse Dynamin 1 GTPase dimer, short axis form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X2F
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-1
- EC
- 3.6.5.5
- UniProt
- Q05193
- Ligands
- GDP, ALF, MG, NA
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynamin-1 (EC 3.6.5.5) | protein | 336 | 48% helix, 14% strand | Q05193 |
| D | Dynamin-1 (EC 3.6.5.5) | protein | 333 | 46% helix, 14% strand | Q05193 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, D
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- NA · Sodium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.87 | 0.90 | 114 | GDP, ALF, MG, NA |
| 2 | 237 | 0.58 | 0.79 | 28 | empty |
| 3 | 57 | 0.45 | 0.84 | 13 | empty |
| 4 | 88 | 0.37 | 0.76 | 22 | empty |
| 5 | 54 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–D · 1495 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
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 Q05193
- Elsewhere: RCSB PDB 2X2F · PDBe 2X2F · UniProt Q05193
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