Research workbench
Cryo-EM structure of human P97 bound to atpgs (conformation III)
Analyse Cryo-EM structure of human P97 bound to atpgs (conformation III) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FTN
- Type
- protein
- Length
- 4,422 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 0.84
Structure
electron microscopy · 1 distinct chain · 38% helix, 10% 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 | 737 | 38% helix, 10% 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, F, B, C, D, E
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 | 937 | 0.84 | 0.85 | 112 | AGS, MG |
| 2 | 984 | 0.83 | 0.84 | 111 | AGS, MG |
| 3 | 1051 | 0.83 | 0.84 | 121 | AGS, MG |
| 4 | 1047 | 0.83 | 0.84 | 120 | AGS, MG |
| 5 | 890 | 0.82 | 0.84 | 122 | AGS, MG |
Interfaces
12 interfaces between chains.
- E–F · 3748 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 3747 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 3746 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 3744 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 3736 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5FTN · Cryo-EM structure of human p97 bound to ATPgS (Conformation III) · 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 5FTN · PDBe 5FTN · UniProt P55072
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.