MolNFT v1 · #59172 · protein + DNA
Insertion ternary complex of dbh DNA polymerase
3BQ1 · DNA polymerase IV: “Insertion ternary complex of dbh DNA polymerase”. X-ray diffraction, 2 ligands (DG3, CA), 2 pockets (best druggability 0.79). MolNFT v1 #59172 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BQ1
- Type
- protein + DNA
- Length
- 367 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q4JB80
- Ligands
- DG3, CA
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 344 | 42% helix, 24% strand | Q4JB80 |
| P | DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3') | dna | 10 | — | — |
| T | DNA (5'- D(*DT*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3') | dna | 13 | — | — |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.79 | 0.83 | 82 | DG3 |
| 2 | 445 | 0.58 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–T · 570 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 470 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–P · 359 Ų buried · 9 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 3BQ1 · PDBe 3BQ1 · UniProt Q4JB80
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