Research workbench
Structure of the ADP-bound vat complex
Analyse Structure of the ADP-bound vat complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G4F
- Type
- protein
- Length
- 4,356 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vcp-like ATPase
- UniProt
- O05209
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, P | Vcp-like ATPase | protein | 726 | 39% helix, 13% strand | O05209 |
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 | 817 | 0.85 | 0.88 | 123 | empty |
| 2 | 672 | 0.84 | 0.88 | 96 | empty |
| 3 | 790 | 0.84 | 0.87 | 109 | empty |
| 4 | 1097 | 0.83 | 0.84 | 128 | empty |
| 5 | 537 | 0.83 | 0.89 | 74 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3424 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 3413 Ų buried · 52 hydrogen bonds · protein-protein
- B–P · 3022 Ų buried · 32 hydrogen bonds · protein-protein
- D–P · 2759 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2578 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
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 O05209
- Elsewhere: RCSB PDB 5G4F · PDBe 5G4F · UniProt O05209
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