Research workbench
DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp, mg and zn
Analyse DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp, mg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F2B
- Type
- protein + DNA
- Length
- 1,025 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA polymerase III alpha chain; 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP…
- EC
- 2.7.7.7
- UniProt
- Q5L0J3
- Ligands
- DGT, MG, ZN, PO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA polymerase III alpha chain (EC 2.7.7.7) | protein | 994 | 44% helix, 16% strand | Q5L0J3 |
| P | 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*D AP*DAP*DCP*DC)-3' | dna | 13 | — | — |
| T | 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*D GP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3' | dna | 18 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.76 | 0.79 | 69 | empty |
| 2 | 856 | 0.74 | 0.78 | 87 | MG, DGT |
| 3 | 553 | 0.69 | 0.79 | 52 | empty |
| 4 | 474 | 0.65 | 0.78 | 57 | MG |
| 5 | 236 | 0.64 | 0.83 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1156 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–P · 719 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–T · 582 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 3F2B · DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn · 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 Q5L0J3
- Elsewhere: RCSB PDB 3F2B · PDBe 3F2B · UniProt Q5L0J3
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