MolNFT v1 · #88868 · protein
Metallosphera sedula VPS4 crystal structure
4D82 · Aaa ATPase, central domain protein: “Metallosphera sedula VPS4 crystal structure”. X-ray diffraction, 1 ligand (ADP), 7 pockets (best druggability 0.68). MolNFT v1 #88868 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4D82
- Type
- protein
- Length
- 813 residues
- Chains
- 3
- 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
- Ligands
- ADP
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 267 | 55% helix, 11% strand | A4YHC5 |
| B | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 274 | 54% helix, 12% strand | A4YHC5 |
| C | Aaa ATPase, central domain protein (EC 3.6.4.6) | protein | 272 | 54% helix, 11% strand | A4YHC5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.68 | 0.75 | 79 | ADP |
| 2 | 381 | 0.61 | 0.77 | 45 | empty |
| 3 | 303 | 0.57 | 0.77 | 27 | empty |
| 4 | 145 | 0.53 | 0.80 | 30 | ADP |
| 5 | 110 | 0.47 | 0.80 | 24 | ADP |
Interfaces
2 interfaces between chains.
- A–B · 981 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 266 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4D82 · 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 4D82 · PDBe 4D82 · UniProt A4YHC5
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