Research workbench
Human P97 single hexamer conformer I with atpgammas bound
Analyse Human P97 single hexamer conformer I with atpgammas bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VCV
- Type
- protein
- Length
- 4,548 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, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, E, D, C, B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 758 | 39% helix, 14% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains A, F, E, D, C, B
- MG · Magnesium ion · metal · 12 copies · chains A, F, E, D, C, B
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 | 1006 | 0.82 | 0.83 | 115 | AGS, MG |
| 2 | 689 | 0.81 | 0.86 | 87 | AGS, MG |
| 3 | 686 | 0.81 | 0.85 | 79 | AGS, MG |
| 4 | 678 | 0.81 | 0.85 | 87 | AGS, MG |
| 5 | 760 | 0.79 | 0.83 | 100 | AGS, MG |
Interfaces
6 interfaces between chains.
- E–D · 3974 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 3967 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 3962 Ų buried · 29 hydrogen bonds · protein-protein
- D–C · 3959 Ų buried · 29 hydrogen bonds · protein-protein
- F–E · 3957 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7VCV · Human p97 single hexamer conformer I with ATPgammaS 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 7VCV · PDBe 7VCV · UniProt P55072
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