Research workbench
Human aaa+ ATPase vcp mutant - T76A, AMP-pnp-bound form, conformation I
Analyse Human aaa+ ATPase vcp mutant - T76A, AMP-pnp-bound form, conformation I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BPA
- Type
- protein
- Length
- 4,452 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, ANP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 39% helix, 17% 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 | 742 | 39% helix, 17% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, F, B, C, D, E
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 | 1197 | 0.84 | 0.85 | 149 | ADP |
| 2 | 1081 | 0.83 | 0.84 | 115 | ADP |
| 3 | 626 | 0.83 | 0.87 | 96 | ADP |
| 4 | 792 | 0.82 | 0.85 | 95 | ADP |
| 5 | 971 | 0.80 | 0.82 | 89 | ANP |
Interfaces
12 interfaces between chains.
- E–F · 3034 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 3030 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 3021 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 3017 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3016 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7BPA · Human AAA+ ATPase VCP mutant - T76A, AMP-PNP-bound form, Conformation I · 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 7BPA · PDBe 7BPA · UniProt P55072
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