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Crystal structure of DNA polymerase III beta subunit from elizabethkingia anophelis
Analyse Crystal structure of DNA polymerase III beta subunit from elizabethkingia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DT6
- Type
- protein
- Length
- 1,494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp
- UniProt
- A0A077EHW1
- Ligands
- CA, NA, CL
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 371 | 22% helix, 44% strand | A0A077EHW1 |
| B | Beta sliding clamp | protein | 371 | 22% helix, 43% strand | A0A077EHW1 |
| C | Beta sliding clamp | protein | 381 | 22% helix, 43% strand | A0A077EHW1 |
| D | Beta sliding clamp | protein | 371 | 22% helix, 43% strand | A0A077EHW1 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.79 | 0.86 | 55 | empty |
| 2 | 576 | 0.68 | 0.78 | 43 | empty |
| 3 | 151 | 0.60 | 0.84 | 26 | empty |
| 4 | 182 | 0.55 | 0.79 | 30 | empty |
| 5 | 212 | 0.54 | 0.78 | 48 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1526 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1137 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1130 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 312 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 190 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 8DT6 · Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A077EHW1
- Elsewhere: RCSB PDB 8DT6 · PDBe 8DT6 · UniProt A0A077EHW1
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