Research workbench
Bacillus stearothermophilus (newly identified strain as yet unnamed) DNA polymerase fragment
Analyse Bacillus stearothermophilus (newly identified strain as yet unnamed) DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XWL
- Type
- protein
- Length
- 580 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I
- EC
- 2.7.7.7
- UniProt
- P52026
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | P52026 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.66 | 0.81 | 42 | empty |
| 2 | 141 | 0.46 | 0.77 | 25 | empty |
| 3 | 157 | 0.45 | 0.76 | 21 | empty |
| 4 | 152 | 0.43 | 0.74 | 21 | empty |
| 5 | 134 | 0.40 | 0.74 | 18 | empty |
Compared structures
- 1XWL · Bacillus stearothermophilus (newly identified strain as yet unnamed) DNA polymerase… · the same entry in another collection · chain A against A, TM-score 1.00
- P52026 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P52026) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P52026
- Elsewhere: RCSB PDB 1XWL · PDBe 1XWL · UniProt P52026
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