Research workbench
Crystal structure of the DNA polymerase III subunit beta from pseudomonas aeruginosa
Analyse Crystal structure of the DNA polymerase III subunit beta from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AMS
- Type
- protein
- Length
- 1,456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp
- UniProt
- Q9I7C4
- Ligands
- PO4
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 363 | 22% helix, 43% strand | Q9I7C4 |
| B | Beta sliding clamp | protein | 363 | 22% helix, 43% strand | Q9I7C4 |
| C | Beta sliding clamp | protein | 364 | 22% helix, 43% strand | Q9I7C4 |
| D | Beta sliding clamp | protein | 366 | 22% helix, 43% strand | Q9I7C4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.72 | 0.98 | 20 | empty |
| 2 | 677 | 0.67 | 0.76 | 70 | empty |
| 3 | 571 | 0.64 | 0.76 | 47 | empty |
| 4 | 63 | 0.58 | 0.89 | 15 | empty |
| 5 | 229 | 0.56 | 0.79 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1308 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1286 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 831 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 751 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6AMS · Crystal structure of the DNA polymerase III subunit beta from Pseudomonas aeruginosa · the same entry in another collection · chain D against D, TM-score 1.00
- Q9I7C4 · AlphaFold monomer V2.0 prediction for beta sliding clamp (Q9I7C4) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q9I7C4
- Elsewhere: RCSB PDB 6AMS · PDBe 6AMS · UniProt Q9I7C4
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