MolNFT v1 · #15939 · protein + DNA
Thymine-thymine mismatch at the polymerase active site
1NJY · DNA primer strand: “Thymine-thymine mismatch at the polymerase active site”. X-ray diffraction, 5 ligands (TTP, GLC, FRU), 9 pockets (best druggability 0.70). MolNFT v1 #15939 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1NJY
- Type
- protein + DNA
- Length
- 604 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primer strand; DNA template strand; DNA polymerase I
- EC
- 2.7.7.7
- UniProt
- P52026
- Ligands
- TTP, GLC, FRU, MG, SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA primer strand | dna | 11 | — | — |
| C | DNA template strand | dna | 13 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 56% helix, 13% strand | P52026 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains A
- 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 · 2 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 | 267 | 0.70 | 0.86 | 33 | empty |
| 2 | 361 | 0.68 | 0.81 | 45 | GLC, FRU |
| 3 | 768 | 0.68 | 0.75 | 71 | TTP, MG |
| 4 | 114 | 0.43 | 0.77 | 21 | empty |
| 5 | 122 | 0.38 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1100 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–A · 832 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 514 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Compared structures
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 1NJY · PDBe 1NJY · UniProt P52026
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