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Ternary structure of the large fragment of taq DNA polymerase bound to an abasic site and a ddgtp
Analyse Ternary structure of the large fragment of taq DNA polymerase bound to an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RRG
- Type
- protein + DNA
- Length
- 560 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- DG3, NA
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 535 | 51% helix, 13% strand | P19821 |
| B | (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3') | dna | 12 | — | — |
| C | (5'-D(*AP*AP*AP*(3DR)P*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3') | dna | 13 | — | — |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · chains A, B
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, C
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.71 | 0.88 | 26 | empty |
| 2 | 834 | 0.70 | 0.76 | 66 | DG3 |
| 3 | 308 | 0.64 | 0.80 | 34 | NA |
| 4 | 180 | 0.48 | 0.76 | 22 | empty |
| 5 | 64 | 0.43 | 0.81 | 17 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 947 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 864 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 576 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3RRG · Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and… · 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 0.99
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 3RRG · PDBe 3RRG · UniProt P19821
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