MolNFT v1 · #141004 · protein + DNA
Large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with the unnatural base M-Fc pair with datp in the active site
5YTC · DNA polymerase I, thermostable: “Large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with the unnatural base…”. X-ray diffraction, 2 ligands (DTP, MG), 7 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 5YTC
- 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)P*(DOC))…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- DTP, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 539 | 52% helix, 13% strand | P19821 |
| B | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC)P*(DOC))- 3') | dna | 12 | — | — |
| C | DNA (5'-D(*AP*AP*AP*(92F) P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | dna | 16 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 938 | 0.79 | 0.82 | 69 | DTP, MG |
| 2 | 216 | 0.68 | 0.86 | 26 | empty |
| 3 | 166 | 0.63 | 0.84 | 19 | empty |
| 4 | 272 | 0.58 | 0.78 | 33 | empty |
| 5 | 115 | 0.40 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1500 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–B · 826 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–C · 576 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5YTC · 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 5YTC · PDBe 5YTC · UniProt P19821
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