Research workbench
VPS4 with cyclic peptide bound in the central pore
Analyse VPS4 with cyclic peptide bound in the central pore in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NDY
- Type
- protein
- Length
- 1,604 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 4; Designed cyclic peptide
- UniProt
- P52917
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 4 | protein | 314 | 42% helix, 11% strand | P52917 |
| B, C, D | Vacuolar protein sorting-associated protein 4 | protein | 322 | 43% helix, 11% strand | P52917 |
| E | Vacuolar protein sorting-associated protein 4 | protein | 304 | 43% helix, 12% strand | P52917 |
| G | Designed cyclic peptide | protein | 20 | 0% helix, 15% 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.79 | 0.82 | 84 | ADP, BEF, MG |
| 2 | 1112 | 0.79 | 0.81 | 96 | ADP, MG |
| 3 | 819 | 0.78 | 0.82 | 70 | ADP, BEF, MG |
| 4 | 692 | 0.77 | 0.82 | 67 | ADP, BEF, MG |
| 5 | 63 | 0.73 | 0.97 | 21 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2102 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 2099 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2093 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2090 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 377 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6NDY · Vps4 with Cyclic Peptide Bound in the Central Pore · 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 0.95
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 P52917
- Elsewhere: RCSB PDB 6NDY · PDBe 6NDY · UniProt P52917
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