Research workbench
Cryo-EM structure of human P97-E470D mutant bound to atpgs.
Analyse Cryo-EM structure of human P97-E470D 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
- 7RLF
- 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 0.79
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 | 615 | 0.79 | 0.84 | 80 | AGS, MG |
| 2 | 627 | 0.79 | 0.84 | 80 | AGS, MG |
| 3 | 479 | 0.78 | 0.86 | 78 | AGS, MG |
| 4 | 619 | 0.78 | 0.84 | 80 | AGS, MG |
| 5 | 399 | 0.78 | 0.87 | 64 | AGS, MG |
Interfaces
12 interfaces between chains.
- B–C · 3741 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 3734 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 3711 Ų buried · 34 hydrogen bonds · protein-protein
- A–F · 3706 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 3704 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7RLF · Cryo-EM structure of human p97-E470D 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 7RLF · PDBe 7RLF · UniProt P55072
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