MolNFT v1 · #143017 · protein
Crystal structure of the DNA polymerase III subunit beta from pseudomonas aeruginosa
6AMS · Beta sliding clamp: “Crystal structure of the DNA polymerase III subunit beta from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (PO4), 17 pockets (best druggability 0.72). MolNFT v1 #143017 on GenesisL1: 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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