MolNFT v1 · #15951 · protein + DNA
A bacillus DNA polymerase I product complex bound to a guanine-thymine mismatch after three rounds of primer extension, following incorporation of dctp, dgtp, and dttp.
1NKB · DNA primer strand: “A bacillus DNA polymerase I product complex bound to a guanine-thymine mismatch after three rounds of primer…”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 10 pockets (best druggability 0.70). MolNFT v1 #15951…
- PDB
- 1NKB
- Type
- protein + DNA
- Length
- 607 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 0.70
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA primer strand | dna | 13 | — | — |
| C | DNA template strand | dna | 14 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 56% helix, 14% strand | P52026 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, C
- 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.70 | 0.82 | 45 | GLC, FRU |
| 2 | 124 | 0.70 | 0.91 | 21 | empty |
| 3 | 381 | 0.64 | 0.78 | 34 | MG |
| 4 | 71 | 0.53 | 0.86 | 15 | empty |
| 5 | 89 | 0.50 | 0.83 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1087 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–A · 873 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 610 Ų buried · 61 hydrogen bonds · nucleic-nucleic
Compared structures
- 1NKB · A bacillus DNA polymerase I product complex bound to a guanine-thymine mismatch after… · 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 1NKB · PDBe 1NKB · UniProt P52026
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