MolNFT v1 · #89112 · protein + DNA
Large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dutp
4DFK · DNA polymerase I, thermostable: “Large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with…”. X-ray diffraction, 2 ligands (0L5, MG), 7 pockets (best druggability 0.80). MolNFT v1 #89112 on…
- PDB
- 4DFK
- Type
- protein + DNA
- Length
- 567 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; 5'-D(GACCACGGCGC doc)-3'; 5'-D(AAAAGGCGCCGTGGTC)-3'
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- 0L5, MG
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 539 | 54% helix, 13% strand | P19821 |
| B | 5'-D(GACCACGGCGC doc)-3' | dna | 12 | — | — |
| C | 5'-D(AAAAGGCGCCGTGGTC)-3' | dna | 16 | — | — |
Ligands and binding sites
- 0L5 · 2'-deoxy-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}uridine 5'-(tetrahydrogen triphosphate) · ligand · chains A, B, C
- MG · Magnesium ion · metal · 6 copies · chains A, B, C
- FMT · Formic acid · additive · 5 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.80 | 0.82 | 72 | 0L5, MG, EDO |
| 2 | 230 | 0.70 | 0.87 | 26 | FMT, MG |
| 3 | 290 | 0.62 | 0.80 | 32 | FMT |
| 4 | 67 | 0.41 | 0.80 | 18 | EDO, FMT |
| 5 | 117 | 0.40 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1431 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 769 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 575 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DFK · large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · 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 P19821
- Elsewhere: RCSB PDB 4DFK · PDBe 4DFK · UniProt P19821
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.