MolNFT v1 · #79442 · protein + DNA
Ternary structure of the large fragment of taq DNA polymerase bound to an abasic site and dnitp
3T3F · DNA polymerase I, thermostable: “Ternary structure of the large fragment of taq DNA polymerase bound to an abasic site and dnitp”. X-ray diffraction, 3 ligands (N5P, MG, NA), 6 pockets (best druggability 0.74). MolNFT v1 #79442 on…
- 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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