Research workbench
Post-insertion binary complex of dbh DNA polymerase
Analyse Post-insertion binary complex of dbh DNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BQ2
- Type
- protein + DNA
- Length
- 364 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DGP*DG)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q4JB80
- Ligands
- CA
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DGP*DG)-3') | dna | 11 | — | — |
| T | DNA (5'- D(*DTP*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3') | dna | 12 | — | — |
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 42% helix, 25% strand | Q4JB80 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.79 | 0.81 | 78 | CA |
| 2 | 432 | 0.58 | 0.75 | 26 | empty |
| 3 | 133 | 0.54 | 0.82 | 18 | empty |
| 4 | 64 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- P–A · 526 Ų buried · 8 hydrogen bonds · protein-nucleic
- P–T · 504 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- T–A · 415 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
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 Q4JB80
- Elsewhere: RCSB PDB 3BQ2 · PDBe 3BQ2 · UniProt Q4JB80
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