Research workbench
Cryo-EM structure of human P97-D592N mutant bound to atpgs.
Analyse Cryo-EM structure of human P97-D592N mutant bound to atpgs. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RLH
- Type
- protein
- Length
- 4,368 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 · 40% 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 | 728 | 40% helix, 16% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains A, F, B, C, D, E
- MG · Magnesium ion · metal · 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 | 985 | 0.82 | 0.83 | 104 | AGS, MG |
| 2 | 748 | 0.81 | 0.85 | 91 | empty |
| 3 | 546 | 0.81 | 0.87 | 96 | AGS, MG |
| 4 | 1148 | 0.81 | 0.82 | 109 | AGS, MG |
| 5 | 545 | 0.81 | 0.87 | 98 | AGS, MG |
Interfaces
12 interfaces between chains.
- C–D · 4015 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 3993 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 3924 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3886 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 3868 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 7RLH · Cryo-EM structure of human p97-D592N mutant bound to ATPgS. · 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 7RLH · PDBe 7RLH · UniProt P55072
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