Research workbench
Structure of vcp dodecamer purified from H1299 cells
Analyse Structure of vcp dodecamer purified from H1299 cells in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K56
- Type
- protein
- Length
- 8,892 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase
- EC
- 3.6.4.6
- UniProt
- P55072
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 35% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 741 | 35% helix, 12% strand | P55072 |
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 | 1061 | 0.84 | 0.85 | 128 | empty |
| 2 | 1153 | 0.84 | 0.85 | 153 | empty |
| 3 | 938 | 0.84 | 0.85 | 121 | empty |
| 4 | 927 | 0.84 | 0.85 | 118 | empty |
| 5 | 941 | 0.83 | 0.85 | 124 | empty |
Interfaces
24 interfaces between chains.
- A–B · 3625 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 3624 Ų buried · 27 hydrogen bonds · protein-protein
- G–L · 3619 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 3619 Ų buried · 27 hydrogen bonds · protein-protein
- J–K · 3619 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7K56 · Structure of VCP dodecamer purified from H1299 cells · the same entry in another collection · chain A against A, 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 P55072
- Elsewhere: RCSB PDB 7K56 · PDBe 7K56 · UniProt P55072
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