Research workbench
Ternary structure of the large fragment of taq DNA polymerase
Analyse Ternary structure of the large fragment of taq DNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DLG
- Type
- protein + DNA
- Length
- 566 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; DNA primer; DNA template
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- DCT, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 540 | 53% helix, 13% strand | P19821 |
| B | DNA primer | dna | 12 | — | — |
| C | DNA template | dna | 14 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B, C
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 | 1192 | 0.77 | 0.79 | 79 | DCT, MG |
| 2 | 212 | 0.71 | 0.88 | 23 | GOL |
| 3 | 271 | 0.60 | 0.79 | 31 | ACT |
| 4 | 141 | 0.55 | 0.81 | 20 | empty |
| 5 | 174 | 0.46 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1157 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 824 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 558 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DLG · Ternary Structure of the large Fragment of Taq DNA polymerase · 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 4DLG · PDBe 4DLG · UniProt P19821
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