Research workbench
Structure of DNA polymerase III subunit beta from rickettsia conorii in complex with a natural product
Analyse Structure of DNA polymerase III subunit beta from rickettsia conorii in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DM6
- Type
- protein
- Length
- 775 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Natural product peptide
- UniProt
- Q92I37
- Ligands
- ACE
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 378 | 23% helix, 43% strand | Q92I37 |
| B | Beta sliding clamp | protein | 377 | 21% helix, 42% strand | Q92I37 |
| C, D | Natural product peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.41 | 0.78 | 16 | empty |
| 2 | 82 | 0.41 | 0.79 | 16 | empty |
| 3 | 56 | 0.30 | 0.75 | 15 | empty |
| 4 | 53 | 0.28 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1195 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 517 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 513 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified, 2 covalent (nonstandard, methylation, covalent ligand).
Compared structures
- 6DM6 · Structure of DNA polymerase III subunit beta from Rickettsia conorii in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92I37 · AlphaFold monomer V2.0 prediction for beta sliding clamp (Q92I37) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q92I37
- Elsewhere: RCSB PDB 6DM6 · PDBe 6DM6 · UniProt Q92I37
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