MolNFT v1 · #21298 · protein
Insight in DNA replication: the crystal structure of DNA polymerase B1 from the archaeon sulfolobus solfataricus
1S5J · DNA polymerase I: “Insight in DNA replication: the crystal structure of DNA polymerase B1 from the archaeon sulfolobus…”. X-ray diffraction, 2 ligands (MG, SO4), 11 pockets (best druggability 0.70). MolNFT v1 #21298 on GenesisL1: 3D…
- PDB
- 1S5J
- Type
- protein
- Length
- 727 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
- P26811
- Ligands
- MG, SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 727 | 39% helix, 20% strand | P26811 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.70 | 0.94 | 22 | empty |
| 2 | 334 | 0.60 | 0.77 | 26 | MG |
| 3 | 235 | 0.58 | 0.79 | 36 | SO4 |
| 4 | 141 | 0.57 | 0.82 | 24 | empty |
| 5 | 265 | 0.57 | 0.78 | 33 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1S5J · Insight in DNA Replication: The crystal structure of DNA Polymerase B1 from the archaeon… · the same entry in another collection · chain A against A, TM-score 1.00
- P26811 · AlphaFold monomer V2.0 prediction for DNA polymerase 1 (P26811) · 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 P26811
- Elsewhere: RCSB PDB 1S5J · PDBe 1S5J · UniProt P26811
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.