MolNFT v1 · #15940 · protein + DNA
Cytosine-thymine mismatch at the polymerase active site
1NJZ · DNA primer strand: “Cytosine-thymine mismatch at the polymerase active site”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 10 pockets (best druggability 0.72). MolNFT v1 #15940 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1NJZ
- Type
- protein + DNA
- Length
- 601 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
- GLC, FRU, MG, SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA primer strand | dna | 10 | — | — |
| C | DNA template strand | dna | 11 | — | — |
| 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 · chains A
- FRU · beta-D-fructofuranose · sugar · 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 | 141 | 0.72 | 0.92 | 21 | empty |
| 2 | 383 | 0.69 | 0.82 | 46 | GLC, FRU |
| 3 | 678 | 0.69 | 0.77 | 61 | SO4, MG |
| 4 | 122 | 0.51 | 0.81 | 15 | empty |
| 5 | 133 | 0.46 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–A · 844 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–A · 823 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 489 Ų buried · 42 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 1NJZ · PDBe 1NJZ · UniProt P52026
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