MolNFT v1 · #89114 · protein + DNA
Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dctp
4DFM · DNA polymerase I, thermostable: “Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in ternary complex with…”. X-ray diffraction, 2 ligands (0L6, MG), 7 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 4DFM
- 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 ddg)-3'; 5'-D(AAAGCGCGCCGTGGTC)-3'
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- 0L6, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 539 | 55% helix, 13% strand | P19821 |
| B | 5'-D(GACCACGGCGC ddg)-3' | dna | 12 | — | — |
| C | 5'-D(AAAGCGCGCCGTGGTC)-3' | dna | 16 | — | — |
Ligands and binding sites
- 0L6 · 5-(5-aminopent-1-yn-1-yl)-2'-deoxycytidine 5'-(tetrahydrogen triphosphate) · ligand · chains A, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C
- FMT · Formic acid · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.79 | 0.82 | 65 | 0L6, MG, EDO |
| 2 | 246 | 0.71 | 0.87 | 28 | MG |
| 3 | 295 | 0.61 | 0.79 | 33 | EDO |
| 4 | 132 | 0.54 | 0.81 | 20 | empty |
| 5 | 151 | 0.44 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1409 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 844 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–C · 597 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DFM · Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in… · 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 4DFM · PDBe 4DFM · UniProt P19821
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