MolNFT v1 · #13188 · protein + DNA
Crystal structure of bacillus DNA polymerase I fragment complexed to 9 base pairs of duplex DNA.
1L3S · 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*G)-3': “Crystal structure of bacillus DNA polymerase I fragment complexed to 9 base pairs of duplex DNA.”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 10 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 1L3S
- Type
- protein + DNA
- Length
- 603 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*G)-3'; 5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)…
- EC
- 2.7.7.7
- UniProt
- P52026
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*G)-3' | dna | 9 | — | — |
| C | 5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3' | dna | 14 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | P52026 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.75 | 0.86 | 36 | empty |
| 2 | 359 | 0.69 | 0.82 | 47 | GLC, FRU |
| 3 | 349 | 0.63 | 0.79 | 36 | MG |
| 4 | 474 | 0.58 | 0.74 | 40 | empty |
| 5 | 154 | 0.46 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1414 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–A · 782 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 442 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 1L3S · Crystal Structure of Bacillus DNA Polymerase I Fragment complexed to 9 base pairs of… · the same entry in another collection · chain B against B, 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 0.99
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 P52026
- Elsewhere: RCSB PDB 1L3S · PDBe 1L3S · UniProt P52026
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