Research workbench
Structure of a VPS23-C:VPS28-N subcomplex
Analyse Structure of a VPS23-C:VPS28-N subcomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F6M
- Type
- protein
- Length
- 337 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
- Ligands
- DDQ, MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Suppressor protein STP22 of temperature-sensitive alpha- factor receptor and arginine permease | protein | 65 | 85% helix, 0% strand | P25604 |
| B | Vacuolar protein sorting-associated protein VPS28 | protein | 107 | 70% helix, 0% strand | Q02767 |
| C | Suppressor protein STP22 of temperature-sensitive alpha- factor receptor and arginine permease | protein | 63 | 86% helix, 0% strand | P25604 |
| D | Vacuolar protein sorting-associated protein VPS28 | protein | 102 | 66% helix, 0% strand | Q02767 |
Ligands and binding sites
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · 8 copies · chains A, C, D, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.70 | 0.78 | 64 | DDQ |
| 2 | 317 | 0.64 | 0.80 | 33 | DDQ |
| 3 | 174 | 0.62 | 0.83 | 20 | empty |
| 4 | 98 | 0.41 | 0.77 | 18 | empty |
| 5 | 98 | 0.38 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1698 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1500 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 430 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2F6M · Structure of a Vps23-C:Vps28-N subcomplex · the same entry in another collection · chain B against B, 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 C against A, TM-score 0.97
- Q02767 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 28… · a predicted model of the same protein · chain D against A, TM-score 0.94
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
- Elsewhere: RCSB PDB 2F6M · PDBe 2F6M · UniProt P25604 · UniProt Q02767
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