Research workbench
Structure of DNA polymerase III subunit beta from Rickettsia typhi in complex with a natural product
Analyse Structure of DNA polymerase III subunit beta from Rickettsia typhi in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DJK
- Type
- protein
- Length
- 386 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Rickettsia typhi str. Wilmington; SYNTHETIC CONSTRUCT
- Molecule
- Beta sliding clamp; ACE-mva-MP8-nzc-leu-MP8-leu-mva-pro-mlu-gly
- UniProt
- Q68WW0
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · resolution 1.85 · 2 distinct chains · 23% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 376 | 23% helix, 44% strand | Q68WW0 |
| B | ACE-mva-MP8-nzc-leu-MP8-leu-mva-pro-mlu-gly | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.38 | 0.78 | 16 | empty |
| 2 | 56 | 0.35 | 0.78 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 514 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard, methylation).
Compared structures
- 6DJK · Structure of DNA polymerase III subunit beta from rickettsia typhi in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q68WW0 · AlphaFold monomer V2.0 prediction for beta sliding clamp (Q68WW0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q68WW0
- Elsewhere: RCSB PDB 6DJK · PDBe 6DJK · UniProt Q68WW0
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