MolNFT v1 · #13257 · protein + DNA
Crystal structure of bacillus DNA polymerase I fragment product complex with 12 base pairs of duplex DNA following addition of a dttp, a datp, and a dctp residue.
1L5U · 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*C)-3': “Crystal structure of bacillus DNA polymerase I fragment product complex with 12 base pairs of duplex DNA…”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 9 pockets (best druggability…
- PDB
- 1L5U
- Type
- protein + DNA
- Length
- 606 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*GP*TP*AP*C)-3'; 5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*…
- EC
- 2.7.7.7
- UniProt
- P52026
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*C)-3' | dna | 12 | — | — |
| 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 | 56% 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 · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.73 | 0.86 | 37 | empty |
| 2 | 731 | 0.69 | 0.77 | 75 | SO4, MG |
| 3 | 397 | 0.68 | 0.81 | 46 | GLC, FRU |
| 4 | 139 | 0.47 | 0.78 | 26 | empty |
| 5 | 104 | 0.35 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1085 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–A · 822 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 550 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 1L5U · Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 12 base… · 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 1L5U · PDBe 1L5U · UniProt P52026
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