Research workbench
Human aaa+ ATPase vcp mutant - T76A, ADP-bound form
Analyse Human aaa+ ATPase vcp mutant - T76A, ADP-bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BP8
- Type
- protein
- Length
- 4,440 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase
- EC
- 3.6.4.6
- UniProt
- P55072
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 740 | 39% helix, 15% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, B, C, D, E, F
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 | 1033 | 0.84 | 0.85 | 118 | ADP |
| 2 | 964 | 0.84 | 0.85 | 108 | ADP |
| 3 | 1178 | 0.84 | 0.85 | 129 | ADP |
| 4 | 547 | 0.82 | 0.88 | 86 | empty |
| 5 | 677 | 0.81 | 0.86 | 76 | empty |
Interfaces
12 interfaces between chains.
- D–E · 3467 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3445 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 3443 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 3441 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 3418 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7BP8 · Human AAA+ ATPase VCP mutant - T76A, ADP-bound form · 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 7BP8 · PDBe 7BP8 · UniProt P55072
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