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Ternary structure of the large fragment of taq DNA polymerase bound to an abasic site and dnitp
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
- 3T3F
- Type
- protein + DNA
- Length
- 558 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*(DOC))-3'…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- N5P, MG, NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 533 | 52% helix, 13% strand | P19821 |
| B | 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3' | dna | 12 | — | — |
| C | 5'-D(*AP*AP*AP*(3DR)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3' | dna | 13 | — | — |
Ligands and binding sites
- N5P · 1-{2-deoxy-5-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro -1H-indole · ligand · chains A, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 13 copies · chains A, C, B
- FMT · Formic acid · additive · 4 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.74 | 0.78 | 62 | MG, N5P |
| 2 | 229 | 0.70 | 0.87 | 25 | GOL |
| 3 | 453 | 0.67 | 0.78 | 42 | empty |
| 4 | 284 | 0.61 | 0.79 | 31 | GOL |
| 5 | 59 | 0.39 | 0.80 | 17 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 912 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 831 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–C · 556 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3T3F · 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 0.98
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 3T3F · PDBe 3T3F · UniProt P19821
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