MolNFT v1 · #189369 · protein
Human P97 single hexamer conformer III with D1-atpgammas and D2-ADP bound
7VCT · Transitional endoplasmic reticulum ATPase: “Human P97 single hexamer conformer III with D1-atpgammas and D2-ADP bound”. Electron microscopy, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #189369 on…
- PDB
- 7VCT
- Type
- protein
- Length
- 4,506 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
- AGS, ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 41% helix, 16% 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 | 751 | 41% helix, 16% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains A, F, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 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 | 1054 | 0.83 | 0.84 | 107 | AGS, MG |
| 2 | 682 | 0.79 | 0.84 | 88 | AGS, MG |
| 3 | 549 | 0.79 | 0.85 | 58 | empty |
| 4 | 1049 | 0.78 | 0.80 | 102 | ADP |
| 5 | 1073 | 0.78 | 0.80 | 113 | ADP |
Interfaces
6 interfaces between chains.
- A–B · 3526 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 3523 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 3519 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 3519 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 3519 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7VCT · Human p97 single hexamer conformer III with D1-ATPgammaS and D2-ADP bound · 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 7VCT · PDBe 7VCT · UniProt P55072
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