MolNFT v1 · #119355 · protein
Cryo-EM structure of human P97 bound to atpgs (conformation II)
5FTM · Transitional endoplasmic reticulum ATPase: “Cryo-EM structure of human P97 bound to atpgs (conformation II)”. Electron microscopy, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #119355 on GenesisL1: 3D…
- PDB
- 5FTM
- 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, ADP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 38% helix, 14% 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 | 38% helix, 14% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains A, F, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, F, B, C, D, E
- MG · Magnesium ion · metal · 6 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 | 974 | 0.82 | 0.84 | 123 | AGS, MG |
| 2 | 713 | 0.82 | 0.86 | 120 | AGS, MG |
| 3 | 925 | 0.82 | 0.84 | 119 | AGS, MG |
| 4 | 768 | 0.81 | 0.84 | 111 | AGS, MG |
| 5 | 480 | 0.79 | 0.87 | 84 | MG |
Interfaces
13 interfaces between chains.
- C–D · 3656 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 3648 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 3648 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 3644 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 3640 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5FTM · Cryo-EM structure of human p97 bound to ATPgS (Conformation II) · 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 5FTM · PDBe 5FTM · UniProt P55072
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.