Research workbench
Binary complex of the large fragment of DNA polymerase I from thermus aquaticus with the aritificial base pair dnam-D5SICS at the postinsertion site (sequence context 3)
Analyse Binary complex of the large fragment of DNA polymerase I from thermus aquaticus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C8N
- Type
- protein + DNA
- Length
- 564 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large fragment of taq DNA polymerase I; Primer…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Large fragment of taq DNA polymerase I (EC 2.7.7.7) | protein | 540 | 56% helix, 13% strand | P19821 |
| B | Primer, 5'-D(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3' | dna | 11 | — | — |
| C | Template, 5'- D(*TP*TP*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-3' | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.76 | 0.96 | 27 | empty |
| 2 | 244 | 0.72 | 0.87 | 30 | empty |
| 3 | 831 | 0.71 | 0.77 | 70 | empty |
| 4 | 275 | 0.62 | 0.80 | 33 | empty |
| 5 | 145 | 0.45 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 982 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–B · 889 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 673 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4C8N · Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the… · 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 0.98
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 4C8N · PDBe 4C8N · UniProt P19821
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