MolNFT v1 · #108027 · protein
Human dynamin 1 K44A superconstricted polymer stabilized with GTP
4UUD · Dynamin-1: “Human dynamin 1 K44A superconstricted polymer stabilized with GTP”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #108027 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UUD
- Type
- protein
- Length
- 2,600 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-1
- EC
- 3.6.5.5
- UniProt
- Q05193
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Dynamin-1 (EC 3.6.5.5) | protein | 329 | 47% helix, 12% strand | Q05193 |
| B, E, I, J | Dynamin-1 (EC 3.6.5.5) | protein | 204 | 80% helix, 0% strand | Q05193 |
| C, F, H, L | Dynamin-1 (EC 3.6.5.5) | protein | 113 | 15% helix, 35% strand | Q05193 |
| D, K | Dynamin-1 (EC 3.6.5.5) | protein | 337 | 45% helix, 13% strand | Q05193 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.78 | 0.80 | 95 | empty |
| 2 | 84 | 0.70 | 0.94 | 21 | empty |
| 3 | 82 | 0.69 | 0.94 | 21 | empty |
| 4 | 399 | 0.67 | 0.79 | 44 | empty |
| 5 | 324 | 0.65 | 0.80 | 30 | empty |
Interfaces
12 interfaces between chains.
- B–J · 1670 Ų buried · 18 hydrogen bonds · protein-protein
- E–I · 1669 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 935 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 489 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 489 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4UUD · Human dynamin 1 K44A superconstricted polymer stabilized with GTP · the same entry in another collection · chain L against L, TM-score 1.00
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 4UUD · PDBe 4UUD · UniProt Q05193
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