MolNFT v2 · #212308 · protein
Structure of heptameric RdrA ring
8HR8 · Archaeal ATPase: “Structure of heptameric RdrA ring”. Electron microscopy at 3.3, 1 ligand (ATP), 20 pockets (best druggability 0.87). MolNFT v2 #212308 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8HR8
- Type
- protein
- Length
- 5,839 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Escherichia coli
- Molecule
- Archaeal ATPase
- UniProt
- A0A8H9B1T2
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.3 · 6 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Archaeal ATPase | protein | 836 | 53% helix, 7% strand | A0A8H9B1T2 |
| C | Archaeal ATPase | protein | 835 | 54% helix, 7% strand | A0A8H9B1T2 |
| E | Archaeal ATPase | protein | 833 | 54% helix, 6% strand | A0A8H9B1T2 |
| F | Archaeal ATPase | protein | 835 | 54% helix, 6% strand | A0A8H9B1T2 |
| G | Archaeal ATPase | protein | 830 | 54% helix, 6% strand | A0A8H9B1T2 |
| H | Archaeal ATPase | protein | 834 | 54% helix, 6% strand | A0A8H9B1T2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, D, C, E, F, G, H
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 | 952 | 0.87 | 0.89 | 129 | empty |
| 2 | 987 | 0.84 | 0.85 | 104 | ATP |
| 3 | 599 | 0.84 | 0.89 | 90 | empty |
| 4 | 669 | 0.84 | 0.88 | 80 | ATP |
| 5 | 572 | 0.83 | 0.89 | 70 | ATP |
Interfaces
12 interfaces between chains.
- E–F · 4855 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 4757 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 4671 Ų buried · 26 hydrogen bonds · protein-protein
- F–G · 4529 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 4393 Ų buried · 32 hydrogen bonds · protein-protein
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 A0A8H9B1T2
- Elsewhere: RCSB PDB 8HR8 · PDBe 8HR8 · UniProt A0A8H9B1T2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.