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
- 6AP1
- Type
- protein
- Length
- 2,404 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 4,PROTEIN HCP1…
- UniProt
- P52917, Q9I747, Q06263
- Ligands
- ADP, BEF, ACE, MG, NH2
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 4,PROTEIN HCP1 | protein | 314 | 42% helix, 10% strand | P52917, Q9I747 |
| B, C, D | Vacuolar protein sorting-associated protein 4,PROTEIN HCP1 | protein | 322 | 44% helix, 11% strand | P52917, Q9I747 |
| E | Vacuolar protein sorting-associated protein 4,PROTEIN HCP1 | protein | 304 | 42% helix, 9% strand | P52917, Q9I747 |
| G | ACE-asp-glu-ile-val-asn-lys-val-leu-NH2 | protein | 8 | 0% helix, 0% strand | — |
| F | Vacuolar protein sorting-associated protein 4,PROTEIN HCP1 | protein | 308 | 49% helix, 13% strand | P52917, Q9I747 |
| H, I, J, K, L, M, N, O, P, Q, R, S | Vacuolar protein sorting-associated protein VTA1 | protein | 42 | 79% helix, 0% strand | Q06263 |
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
- ACE · Acetyl group · ligand · chains A, G
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E
- NH2 · Amino group · ion · chains G
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 | 923 | 0.81 | 0.83 | 99 | ADP, BEF, MG |
| 2 | 999 | 0.80 | 0.81 | 102 | ADP, MG |
| 3 | 1086 | 0.79 | 0.81 | 106 | ADP, BEF, MG |
| 4 | 901 | 0.79 | 0.81 | 87 | ADP, BEF, MG |
| 5 | 716 | 0.73 | 0.79 | 60 | empty |
Interfaces
35 interfaces between chains.
- A–B · 2041 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 2009 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 2007 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1983 Ų buried · 10 hydrogen bonds · protein-protein
- J–K · 1001 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6AP1 · Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p · the same entry in another collection · chain J against J, TM-score 1.00
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
- Every structure of UniProt Q9I747
- Every structure of UniProt Q06263
- Elsewhere: RCSB PDB 6AP1 · PDBe 6AP1 · UniProt P52917 · UniProt Q9I747 · UniProt Q06263
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