MolNFT v1 · #87686 · protein + DNA
Binary complex of the large fragment of DNA polymerase I from thermus aquaticus with the aritificial base pair D5SICS-dnam at the postinsertion site (sequence context 2)
4C8M · Large fragment of taq DNA polymerase I: “Binary complex of the large fragment of DNA polymerase I from thermus aquaticus with the aritificial base…”. X-ray diffraction, 2 ligands (MG, SO4), 4 pockets (best druggability 0.78). MolNFT…
- PDB
- 4C8M
- 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
- MG, SO4
- Pockets
- 4 · best druggability 0.78
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(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*BMNP)-3' | dna | 11 | — | — |
| C | Template, 5'-D(*TP*TP*CP* LHOP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3' | dna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.78 | 0.80 | 86 | GOL |
| 2 | 519 | 0.77 | 0.84 | 67 | empty |
| 3 | 244 | 0.71 | 0.87 | 28 | empty |
| 4 | 191 | 0.49 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 873 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 797 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 597 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4C8M · Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the… · the same entry in another collection · chain C against C, 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 4C8M · PDBe 4C8M · UniProt P19821
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