MolNFT v1 · #136091 · protein
VPS4-VTA1 complex
5UIE · Vacuolar protein sorting-associated protein 4: “VPS4-VTA1 complex”. Electron microscopy, 4 ligands (ADP, BEF, ACE), 20 pockets (best druggability 0.84). MolNFT v1 #136091 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UIE
- Type
- protein
- Length
- 2,386 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 4; DOA4-independent degradation protein 4…
- UniProt
- P52917, Q06263
- Ligands
- ADP, BEF, ACE, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 4 | protein | 312 | 42% helix, 10% strand | P52917 |
| B, C, D | Vacuolar protein sorting-associated protein 4 | protein | 311 | 42% helix, 10% strand | P52917 |
| E | Vacuolar protein sorting-associated protein 4 | protein | 308 | 44% helix, 10% strand | P52917 |
| F | Vacuolar protein sorting-associated protein 4 | protein | 302 | 50% helix, 14% strand | P52917 |
| G | DOA4-independent degradation protein 4 | protein | 8 | 0% helix, 0% strand | — |
| H, J, L, N, O, P, Q, R, S | Vacuolar protein sorting-associated protein VTA1 | protein | 42 | 79% helix, 0% strand | Q06263 |
| I | Vacuolar protein sorting-associated protein VTA1 | protein | 51 | 88% helix, 0% strand | Q06263 |
| K, M | Vacuolar protein sorting-associated protein VTA1 | protein | 47 | 87% 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 · 3 copies · chains A, B, C, D
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 | 918 | 0.84 | 0.86 | 105 | ADP |
| 2 | 1118 | 0.80 | 0.82 | 108 | ADP, BEF, MG |
| 3 | 758 | 0.80 | 0.84 | 83 | ADP, MG, BEF |
| 4 | 776 | 0.79 | 0.83 | 110 | empty |
| 5 | 877 | 0.79 | 0.81 | 79 | ADP, BEF, MG |
Interfaces
36 interfaces between chains.
- B–C · 2311 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2234 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2228 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1910 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1068 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5UIE · Vps4-Vta1 complex · the same entry in another collection · chain L against L, 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 Q06263
- Elsewhere: RCSB PDB 5UIE · PDBe 5UIE · UniProt P52917 · UniProt Q06263
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