Research workbench
Crystal structure of DNA polymerase III, beta chain (ec 2.7.7.7) (NP_344555.1) from streptococcus pneumoniae TIGR4 at 2.50 a resolution
Analyse Crystal structure of DNA polymerase III, beta chain (ec 2.7.7.7) (NP_344555.1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AWA
- Type
- protein
- Length
- 1,509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III, beta chain
- EC
- 2.7.7.7
- UniProt
- O06672
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA polymerase III, beta chain (EC 2.7.7.7) | protein | 377 | 23% helix, 42% strand | O06672 |
| B | DNA polymerase III, beta chain (EC 2.7.7.7) | protein | 378 | 23% helix, 42% strand | O06672 |
| D | DNA polymerase III, beta chain (EC 2.7.7.7) | protein | 377 | 23% helix, 41% strand | O06672 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.69 | 0.78 | 48 | empty |
| 2 | 238 | 0.47 | 0.73 | 25 | empty |
| 3 | 164 | 0.45 | 0.75 | 18 | empty |
| 4 | 92 | 0.42 | 0.78 | 16 | empty |
| 5 | 104 | 0.42 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1127 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1103 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 87 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2AWA · Crystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) (np_344555.1) from… · the same entry in another collection · chain D against D, TM-score 1.00
- O06672 · AlphaFold monomer V2.0 prediction for beta sliding clamp (O06672) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O06672
- Elsewhere: RCSB PDB 2AWA · PDBe 2AWA · UniProt O06672
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.