Research workbench
Cryo-EM structure of human P97-R191Q mutant bound to ADP.
Analyse Cryo-EM structure of human P97-R191Q mutant bound to ADP. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RL9
- Type
- protein
- Length
- 4,464 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
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 38% helix, 8% 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 | 744 | 38% helix, 8% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 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 | 922 | 0.85 | 0.87 | 109 | empty |
| 2 | 908 | 0.85 | 0.86 | 95 | empty |
| 3 | 628 | 0.84 | 0.88 | 89 | empty |
| 4 | 802 | 0.83 | 0.86 | 93 | empty |
| 5 | 865 | 0.83 | 0.85 | 106 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3850 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 3823 Ų buried · 45 hydrogen bonds · protein-protein
- A–F · 3812 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 3809 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3798 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7RL9 · Cryo-EM structure of human p97-R191Q mutant bound to ADP. · 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 7RL9 · PDBe 7RL9 · UniProt P55072
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