MolNFT v1 · #119719 · protein
H.PYLORI beta clamp in complex with 5-chloroisatin
5G4Q · DNA polymerase III subunit beta: “H.PYLORI beta clamp in complex with 5-chloroisatin”. X-ray diffraction, 1 ligand (2HQ), 5 pockets (best druggability 0.58). MolNFT v1 #119719 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5G4Q
- Type
- protein
- Length
- 733 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta
- EC
- 2.7.7.7
- UniProt
- O25242
- Ligands
- 2HQ
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 364 | 20% helix, 42% strand | O25242 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 369 | 21% helix, 41% strand | O25242 |
Ligands and binding sites
- 2HQ · 5-chloro-1H-indole-2,3-dione · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.58 | 0.75 | 51 | empty |
| 2 | 345 | 0.57 | 0.76 | 42 | empty |
| 3 | 114 | 0.39 | 0.75 | 25 | empty |
| 4 | 51 | 0.30 | 0.76 | 16 | empty |
| 5 | 70 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 422 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 O25242
- Elsewhere: RCSB PDB 5G4Q · PDBe 5G4Q · UniProt O25242
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