MolNFT v1 · #14011 · protein + DNA
Crystal structure of the closed conformation of bacillus DNA polymerase I fragment bound to DNA and dctp
1LV5 · 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3': “Crystal structure of the closed conformation of bacillus DNA polymerase I fragment bound to DNA and dctp”. X-ray diffraction, 4 ligands (DCP, MN, MG), 19 pockets (best druggability 0.80).…
- PDB
- 1LV5
- Type
- protein + DNA
- Length
- 1,208 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3'; 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)…
- EC
- 2.7.7.7
- UniProt
- P52026
- Ligands
- DCP, MN, MG, SO4
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' | dna | 10 | — | — |
| D, F | 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)- 3' | dna | 14 | — | — |
| A, B | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 53% helix, 12% strand | P52026 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains C, D, A, E, F, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains C, A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.80 | 0.82 | 81 | DCP |
| 2 | 734 | 0.80 | 0.84 | 66 | empty |
| 3 | 419 | 0.75 | 0.85 | 51 | MN, MG, DCP |
| 4 | 301 | 0.69 | 0.84 | 32 | empty |
| 5 | 173 | 0.68 | 0.88 | 19 | empty |
Interfaces
10 interfaces between chains.
- D–A · 1135 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–B · 1115 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–B · 792 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–A · 792 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 753 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1LV5 · Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound… · 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 0.96
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 1LV5 · PDBe 1LV5 · UniProt P52026
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