Research workbench
Ddgtp-trapped closed ternary complex of the large fragment of DNA polymerase I from thermus aquaticus
Analyse Ddgtp-trapped closed ternary complex of the large fragment of DNA polymerase I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QSS
- Type
- protein + DNA
- Length
- 565 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3'…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- DG3, MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3' | dna | 12 | — | — |
| C | 5'-D(*AP*CP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' | dna | 14 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 539 | 55% helix, 14% strand | P19821 |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · chains B, C, A
- 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.72 | 0.83 | 40 | MG, DG3 |
| 2 | 226 | 0.69 | 0.86 | 26 | empty |
| 3 | 693 | 0.62 | 0.73 | 43 | empty |
| 4 | 258 | 0.59 | 0.79 | 33 | empty |
| 5 | 173 | 0.46 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1094 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–A · 848 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–C · 576 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1QSS · Ddgtp-trapped closed ternary complex of the large fragment of DNA polymerase I from… · the same entry in another collection · chain B against B, 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 1QSS · PDBe 1QSS · UniProt P19821
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