Research workbench
Crystal structure of DNA polymerase III subunit beta from rickettsia conorii
Analyse Crystal structure of DNA polymerase III subunit beta from rickettsia conorii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W7Z
- Type
- protein
- Length
- 761 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
- Q92I37
- Pockets
- 9 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 380 | 22% helix, 44% strand | Q92I37 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 381 | 23% helix, 41% strand | Q92I37 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.43 | 0.80 | 18 | empty |
| 2 | 97 | 0.43 | 0.79 | 16 | empty |
| 3 | 70 | 0.37 | 0.77 | 16 | MRD |
| 4 | 54 | 0.33 | 0.78 | 14 | EDO |
| 5 | 61 | 0.32 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1231 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5W7Z · Crystal structure of DNA polymerase III subunit beta from Rickettsia conorii · 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 A 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 5W7Z · PDBe 5W7Z · UniProt Q92I37
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