Research workbench
Human P97 double hexamer conformer II with atpgammas bound
Analyse Human P97 double hexamer conformer II 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
- 7VCS
- Type
- protein
- Length
- 9,192 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
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 40% helix, 15% 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 | 766 | 40% helix, 15% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 24 copies · chains A, F, B, C, D, E, G, L, H, I, J, K
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 1027 | 0.84 | 0.85 | 138 | AGS, MG |
| 2 | 1034 | 0.84 | 0.85 | 124 | AGS, MG |
| 3 | 917 | 0.83 | 0.85 | 124 | AGS, MG |
| 4 | 873 | 0.82 | 0.84 | 110 | empty |
| 5 | 803 | 0.81 | 0.84 | 93 | AGS |
Interfaces
24 interfaces between chains.
- H–I · 4220 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4186 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 4021 Ų buried · 34 hydrogen bonds · protein-protein
- G–L · 3968 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 3928 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7VCS · Human p97 double hexamer conformer II 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 7VCS · PDBe 7VCS · UniProt P55072
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