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 2)
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
- 4C8O
- Type
- protein + DNA
- Length
- 563 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; 5'-D(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- MG, SO4, CL
- Pockets
- 5 · best druggability 0.75
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 | 540 | 54% helix, 13% strand | P19821 |
| B | 5'-D(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3' | dna | 11 | — | — |
| C | 5'-D(*TP*TP*CP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3' | dna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal
- SO4 · Sulfate ion · ion · 7 copies · chains A
- CL · Chloride ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.75 | 0.93 | 23 | empty |
| 2 | 1070 | 0.73 | 0.77 | 77 | SO4 |
| 3 | 211 | 0.71 | 0.88 | 26 | empty |
| 4 | 257 | 0.62 | 0.81 | 39 | SO4 |
| 5 | 138 | 0.45 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 853 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 729 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 625 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4C8O · 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 4C8O · PDBe 4C8O · UniProt P19821
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