MolNFT v1 · #143015 · protein
Crystal structure of the DNA polymerase III subunit beta from enterobacter cloacae
6AMQ: “Crystal structure of the DNA polymerase III subunit beta from enterobacter cloacae”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.71). MolNFT v1 #143015 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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