MolNFT v1 · #77849 · protein + DNA
Binary structure of the large fragment of taq DNA polymerase bound to an abasic site
3RR7 · DNA polymerase I, thermostable: “Binary structure of the large fragment of taq DNA polymerase bound to an abasic site”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.69). MolNFT v1 #77849 on GenesisL1: 3D…
- PDB
- 3RR7
- Type
- protein + DNA
- Length
- 547 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
- MG
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 520 | 49% 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 | 15 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- FMT · Formic acid · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.69 | 0.87 | 28 | empty |
| 2 | 618 | 0.64 | 0.75 | 63 | GOL, MG |
| 3 | 311 | 0.61 | 0.79 | 34 | empty |
| 4 | 262 | 0.57 | 0.78 | 31 | empty |
| 5 | 61 | 0.38 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1130 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 777 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 600 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3RR7 · Binary Structure of the large fragment of Taq DNA polymerase bound to an abasic site · 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 0.99
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 3RR7 · PDBe 3RR7 · UniProt P19821
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