Research workbench
Binary structure of the large fragment of taq DNA polymerase bound to an abasic site
Analyse Binary structure of the large fragment of taq DNA polymerase bound to an abasic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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