Research workbench
2 ångström X-ray structure of the yeast escrt-I VPS28 C-terminus in complex with the nzf-N domain from escrt-II
Analyse 2 ångström X-ray structure of the yeast escrt-I VPS28 C-terminus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J9U
- Type
- protein
- Length
- 282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 28; Vacuolar protein sorting-associated…
- UniProt
- Q02767, Q06696
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Vacuolar protein sorting-associated protein 28 | protein | 94 | 74% helix, 2% strand | Q02767 |
| B, D | Vacuolar protein sorting-associated protein 36 | protein | 47 | 15% helix, 23% strand | Q06696 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.56 | 0.75 | 37 | empty |
Interfaces
3 interfaces between chains.
- C–D · 517 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 514 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2J9U · 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02767 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 28… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q06696 · AlphaFold monomer V2.0 prediction for vacuolar protein-sorting- associated protein 36… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q02767
- Every structure of UniProt Q06696
- Elsewhere: RCSB PDB 2J9U · PDBe 2J9U · UniProt Q02767 · UniProt Q06696
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