Research workbench
Structure of the yeast escrt-I heterotetramer core
Analyse Structure of the yeast escrt-I heterotetramer core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P22
- Type
- protein
- Length
- 525 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Suppressor protein STP22 of temperature-sensitive alpha- factor receptor and arginine…
- UniProt
- P25604, Q02767, Q99176, P42939
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.28
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Suppressor protein STP22 of temperature-sensitive alpha- factor receptor and arginine permease | protein | 168 | 83% helix, 1% strand | P25604 |
| B | Vacuolar protein sorting-associated protein 28 | protein | 92 | 62% helix, 0% strand | Q02767 |
| C | Protein SRN2 | protein | 186 | 77% helix, 1% strand | Q99176 |
| D | Hypothetical 12.0 kda protein in ADE3-SER2 intergenic region | protein | 79 | 57% helix, 3% strand | P42939 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.28 | 0.73 | 11 | empty |
| 2 | 56 | 0.27 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–C · 3841 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2610 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1729 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1717 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 88 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2P22 · Structure of the Yeast ESCRT-I Heterotetramer Core · the same entry in another collection · chain C against C, TM-score 1.00
- P25604 · AlphaFold monomer V2.0 prediction for suppressor protein STP22 of temperature-sensitive… · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q02767 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 28… · a predicted model of the same protein · chain B against A, TM-score 0.80
- Q99176 · AlphaFold monomer V2.0 prediction for protein SRN2 (Q99176) · a predicted model of the same protein · chain C against A, TM-score 0.68
- P42939 · AlphaFold monomer V2.0 prediction for multivesicular body sorting factor 12 (P42939) · a predicted model of the same protein · chain D against A, TM-score 0.60
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 P25604
- Every structure of UniProt Q02767
- Every structure of UniProt Q99176
- Every structure of UniProt P42939
- Elsewhere: RCSB PDB 2P22 · PDBe 2P22 · UniProt P25604 · UniProt Q02767 · UniProt Q99176 · UniProt P42939
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