Research workbench
Crystal structure of bacillus DNA polymerase I large fragment bound to duplex DNA with cytosine-adenine mismatch at (N-6) position
Analyse Crystal structure of bacillus DNA polymerase I large fragment bound to duplex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TAR
- Type
- protein + DNA
- Length
- 611 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*CP*GP*TP*C)-3'…
- EC
- 2.7.7.7
- UniProt
- C9RTX7
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 56% helix, 13% strand | C9RTX7 |
| B | 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*CP*GP*TP*C)-3' | dna | 15 | — | — |
| C | 5'-D(*GP*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3' | dna | 16 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.72 | 0.85 | 31 | empty |
| 2 | 380 | 0.68 | 0.81 | 45 | GLC, FRU |
| 3 | 345 | 0.62 | 0.79 | 37 | SO4, MG |
| 4 | 136 | 0.48 | 0.78 | 22 | empty |
| 5 | 192 | 0.48 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 930 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 828 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 710 Ų buried · 67 hydrogen bonds · nucleic-nucleic
Compared structures
- 3TAR · Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with… · the same entry in another collection · chain A against A, TM-score 1.00
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 C9RTX7
- Elsewhere: RCSB PDB 3TAR · PDBe 3TAR · UniProt C9RTX7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.