MolNFT v1 · #113038 · protein
Crystal structure of the dynamin tetramer
5A3F · Dynamin 3: “Crystal structure of the dynamin tetramer”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #113038 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5A3F
- Type
- protein
- Length
- 2,500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin 3
- EC
- 3.6.5.5
- UniProt
- Q9UQ16
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynamin 3 (EC 3.6.5.5) | protein | 691 | 50% helix, 14% strand | Q9UQ16 |
| B | Dynamin 3 (EC 3.6.5.5) | protein | 555 | 61% helix, 8% strand | Q9UQ16 |
| C | Dynamin 3 (EC 3.6.5.5) | protein | 700 | 49% helix, 14% strand | Q9UQ16 |
| D | Dynamin 3 (EC 3.6.5.5) | protein | 554 | 61% helix, 8% strand | Q9UQ16 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.83 | 0.84 | 130 | empty |
| 2 | 1179 | 0.81 | 0.83 | 138 | empty |
| 3 | 1013 | 0.81 | 0.83 | 80 | empty |
| 4 | 512 | 0.75 | 0.83 | 76 | empty |
| 5 | 499 | 0.74 | 0.82 | 64 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1450 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1436 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1173 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1144 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1058 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 Q9UQ16
- Elsewhere: RCSB PDB 5A3F · PDBe 5A3F · UniProt Q9UQ16
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