Research workbench
Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Analyse Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BMF
- Type
- protein
- Length
- 1,407 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Saccharomyces cerevisiae; SYNTHETIC CONSTRUCT
- Molecule
- Vacuolar protein sorting-associated protein 4; Vps2p
- UniProt
- P52917
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.2 · 4 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 4 | protein | 277 | 47% helix, 8% strand | P52917 |
| B, C, D | Vacuolar protein sorting-associated protein 4 | protein | 285 | 49% helix, 9% strand | P52917 |
| E | Vacuolar protein sorting-associated protein 4 | protein | 267 | 47% helix, 7% strand | P52917 |
| G | Vps2p | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.81 | 0.82 | 95 | ADP, BEF, MG |
| 2 | 1006 | 0.80 | 0.81 | 94 | ADP, BEF, MG |
| 3 | 1017 | 0.80 | 0.81 | 93 | ADP, BEF, MG |
| 4 | 1122 | 0.78 | 0.80 | 104 | ADP, MG |
| 5 | 383 | 0.64 | 0.79 | 43 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1947 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1906 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1901 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1870 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 296 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6BMF · VPS4P-VTA1P complex with peptide binding to the central pore of VPS4P · the same entry in another collection · chain G against G, 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 E against A, TM-score 0.96
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 6BMF · PDBe 6BMF · UniProt P52917
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.