Research workbench
Crystal structure of the DNA polymerase III subunit beta from enterobacter cloacae
Analyse Crystal structure of the DNA polymerase III subunit beta from enterobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AMQ
- Type
- protein
- Length
- 1,442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta
- UniProt
- G8LES0
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta | protein | 359 | 23% helix, 45% strand | G8LES0 |
| B | DNA polymerase III subunit beta | protein | 365 | 22% helix, 45% strand | G8LES0 |
| C | DNA polymerase III subunit beta | protein | 359 | 23% helix, 43% strand | G8LES0 |
| D | DNA polymerase III subunit beta | protein | 359 | 23% helix, 45% strand | G8LES0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.71 | 0.81 | 56 | empty |
| 2 | 462 | 0.63 | 0.76 | 49 | empty |
| 3 | 424 | 0.60 | 0.76 | 40 | empty |
| 4 | 183 | 0.56 | 0.80 | 34 | empty |
| 5 | 98 | 0.42 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1359 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1277 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 907 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6AMQ · Crystal structure of the DNA polymerase III subunit beta from Enterobacter cloacae · 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 G8LES0
- Elsewhere: RCSB PDB 6AMQ · PDBe 6AMQ · UniProt G8LES0
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