MolNFT v1 · #62536 · protein
Crystal structure of S.CEREVISIAE VPS4 in the presence of atpgammas
3EIH · Vacuolar protein sorting-associated protein 4: “Crystal structure of S.CEREVISIAE VPS4 in the presence of atpgammas”. X-ray diffraction, 2 ligands (AGS, MG), 10 pockets (best druggability 0.65). MolNFT v1 #62536 on GenesisL1: 3D…
- PDB
- 3EIH
- Type
- protein
- Length
- 945 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 4
- UniProt
- P52917
- Ligands
- AGS, MG
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 4 | protein | 319 | 46% helix, 13% strand | P52917 |
| B | Vacuolar protein sorting-associated protein 4 | protein | 316 | 39% helix, 13% strand | P52917 |
| C | Vacuolar protein sorting-associated protein 4 | protein | 310 | 39% helix, 11% strand | P52917 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.65 | 0.87 | 18 | empty |
| 2 | 241 | 0.55 | 0.77 | 25 | empty |
| 3 | 137 | 0.53 | 0.81 | 23 | empty |
| 4 | 86 | 0.50 | 0.83 | 18 | empty |
| 5 | 223 | 0.49 | 0.75 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3EIH · Crystal structure of S.cerevisiae Vps4 in the presence of ATPgammaS · the same entry in another collection · chain A against A, TM-score 1.00
- P52917 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 4… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P52917
- Elsewhere: RCSB PDB 3EIH · PDBe 3EIH · UniProt P52917
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