MolNFT v1 · #141008 · protein + DNA
Structure of large fragment of DNA polymerase I from thermus aquaticus host-guest complex with the unnatural base I-Fc pair with da
5YTG · DNA polymerase I, thermostable: “Structure of large fragment of DNA polymerase I from thermus aquaticus host-guest complex with the unnatural…”. X-ray diffraction, 2 ligands (DGT, MG), 7 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5YTG
- 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; DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- DGT, MG
- Pockets
- 7 · best druggability 0.77
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 | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') | dna | 12 | — | — |
| C | DNA (5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*(94O) P*GP*GP*TP*C)-3') | dna | 16 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · 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 | 1049 | 0.77 | 0.80 | 78 | DGT, MG |
| 2 | 231 | 0.70 | 0.86 | 28 | empty |
| 3 | 265 | 0.60 | 0.79 | 31 | empty |
| 4 | 137 | 0.51 | 0.79 | 17 | empty |
| 5 | 73 | 0.40 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1407 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 849 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 591 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5YTG · Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest 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 0.97
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 5YTG · PDBe 5YTG · UniProt P19821
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