Research workbench
Structure of apo vcp dodecamer generated from bacterially recombinant VCP/P97
Analyse Structure of apo vcp dodecamer generated from bacterially recombinant VCP/P97 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K57
- 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 0.85
Structure
electron microscopy · 1 distinct chain · 34% helix, 13% 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 | 34% helix, 13% 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 | 1174 | 0.85 | 0.86 | 137 | empty |
| 2 | 1177 | 0.85 | 0.86 | 134 | empty |
| 3 | 773 | 0.81 | 0.84 | 77 | empty |
| 4 | 1044 | 0.81 | 0.82 | 99 | empty |
| 5 | 687 | 0.80 | 0.85 | 68 | empty |
Interfaces
24 interfaces between chains.
- H–I · 3406 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 3383 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3383 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 3376 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 3367 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7K57 · Structure of apo VCP dodecamer generated from bacterially recombinant VCP/p97 · 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 7K57 · PDBe 7K57 · UniProt P55072
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