MolNFT v1 · #84905 · protein
Human dynamin 1 deltaprd polymer stabilized with gmppcp
3ZYS · Dynamin-1: “Human dynamin 1 deltaprd polymer stabilized with gmppcp”. Electron microscopy, 9 pockets (best druggability 0.70). MolNFT v1 #84905 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZYS
- Type
- protein
- Length
- 1,316 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-1; Interferon-induced GTP-binding protein MX1
- EC
- 3.6.5.5
- UniProt
- Q05193, P20591
- Pockets
- 9 · best druggability 0.70
Structure
electron microscopy · 4 distinct chains · 60% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dynamin-1 (EC 3.6.5.5) | protein | 330 | 47% helix, 14% strand | Q05193 |
| B | Interferon-induced GTP-binding protein MX1 | protein | 211 | 83% helix, 0% strand | P20591 |
| C, F | Dynamin-1 (EC 3.6.5.5) | protein | 113 | 15% helix, 41% strand | Q05193 |
| E | Interferon-induced GTP-binding protein MX1 | protein | 219 | 81% helix, 0% strand | P20591 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.70 | 0.96 | 24 | empty |
| 2 | 61 | 0.57 | 0.89 | 18 | empty |
| 3 | 140 | 0.53 | 0.80 | 25 | empty |
| 4 | 53 | 0.52 | 0.88 | 16 | empty |
| 5 | 77 | 0.45 | 0.81 | 25 | empty |
Interfaces
4 interfaces between chains.
- D–E · 435 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 95 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 81 Ų buried · 1 hydrogen bond · protein-protein
- B–E · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZYS · Human dynamin 1 deltaPRD polymer stabilized with GMPPCP · the same entry in another collection · chain F against F, TM-score 1.00
- Q05193 · AlphaFold monomer V2.0 prediction for dynamin-1 (Q05193) · a predicted model of the same protein · chain F against A, TM-score 0.90
- P20591 · AlphaFold monomer V2.0 prediction for interferon-induced GTP-binding protein MX1 (P20591) · a predicted model of the same protein · chain E against A, TM-score 0.77
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
- Every structure of UniProt P20591
- Elsewhere: RCSB PDB 3ZYS · PDBe 3ZYS · UniProt Q05193 · UniProt P20591
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