Research workbench
Dynamin 1 GTPase ged fusion dimer complexed with gmppcp
Analyse Dynamin 1 GTPase ged fusion dimer complexed with gmppcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZYC
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-1
- UniProt
- Q05193
- Ligands
- GCP, MG
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynamin-1 | protein | 330 | 47% helix, 14% strand | Q05193 |
| D | Dynamin-1 | protein | 340 | 48% helix, 14% strand | Q05193 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, D
- MG · Magnesium 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.86 | 0.87 | 154 | GCP, MG |
| 2 | 75 | 0.54 | 0.86 | 20 | empty |
| 3 | 120 | 0.52 | 0.81 | 23 | empty |
| 4 | 163 | 0.50 | 0.77 | 29 | empty |
| 5 | 62 | 0.36 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–D · 1459 Ų buried · 22 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 Q05193
- Elsewhere: RCSB PDB 3ZYC · PDBe 3ZYC · UniProt Q05193
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.