MolNFT v1 · #88866 · protein
Metallosphera sedula VPS4 crystal structure
4D80 · Aaa ATPase, central domain protein: “Metallosphera sedula VPS4 crystal structure”. X-ray diffraction, 17 pockets (best druggability 0.81). MolNFT v1 #88866 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4D80
- Type
- protein
- Length
- 1,607 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aaa ATPase, central domain protein
- EC
- 3.6.4.6
- UniProt
- A4YHC5
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 269 | 50% helix, 9% strand | A4YHC5 |
| B | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 257 | 53% helix, 10% strand | A4YHC5 |
| C | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 272 | 53% helix, 9% strand | A4YHC5 |
| D | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 273 | 49% helix, 9% strand | A4YHC5 |
| E | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 262 | 52% helix, 10% strand | A4YHC5 |
| F | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 274 | 51% helix, 9% strand | A4YHC5 |
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.81 | 0.82 | 103 | empty |
| 2 | 927 | 0.80 | 0.82 | 102 | empty |
| 3 | 1107 | 0.80 | 0.81 | 106 | empty |
| 4 | 852 | 0.77 | 0.81 | 91 | empty |
| 5 | 1140 | 0.77 | 0.79 | 92 | empty |
Interfaces
6 interfaces between chains.
- A–F · 1504 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1331 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1221 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1055 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1021 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4D80 · Metallosphera sedula Vps4 crystal structure · the same entry in another collection · chain A against A, 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 A4YHC5
- Elsewhere: RCSB PDB 4D80 · PDBe 4D80 · UniProt A4YHC5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.