Research workbench
Human P97 double hexamer conformer I with D1-atpgammas and D2-ADP bound
Analyse Human P97 double hexamer conformer I with D1-atpgammas and D2-ADP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VCU
- Type
- protein
- Length
- 9,084 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, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, B, C, D, E, F, A, L, G, H, I, J | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 757 | 41% helix, 17% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains K, J, B, A, C, D, E, F, L, G, H, I
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains K, B, C, D, E, F, A, L, G, H, I, J
- MG · Magnesium ion · metal · 12 copies · chains K, B, C, D, E, F, A, L, G, H, I, J
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 | 1053 | 0.85 | 0.85 | 116 | empty |
| 2 | 1075 | 0.84 | 0.85 | 140 | AGS, MG |
| 3 | 970 | 0.84 | 0.86 | 114 | empty |
| 4 | 983 | 0.84 | 0.85 | 108 | AGS |
| 5 | 607 | 0.84 | 0.89 | 87 | empty |
Interfaces
30 interfaces between chains.
- L–G · 3919 Ų buried · 47 hydrogen bonds · protein-protein
- K–J · 3732 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 3702 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 3672 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 3638 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7VCU · Human p97 double hexamer conformer I 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 7VCU · PDBe 7VCU · UniProt P55072
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