Research workbench
DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp, mn and zn
Analyse DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp, mn… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F2D
- Type
- protein + DNA
- Length
- 1,024 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*D AP*DAP*DCP*DC)-3'…
- EC
- 2.7.7.7
- UniProt
- Q5L0J3
- Ligands
- DGT, MN, ZN, PO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 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 | — | — |
| A | Geobacillus kaustophilus DNA polc (EC 2.7.7.7) | protein | 993 | 44% helix, 16% strand | Q5L0J3 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains P, T, A
- MN · Manganese (II) ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.77 | 0.79 | 81 | empty |
| 2 | 735 | 0.73 | 0.79 | 87 | MN, ZN, PO4 |
| 3 | 530 | 0.69 | 0.79 | 50 | empty |
| 4 | 343 | 0.68 | 0.82 | 34 | MN, DGT |
| 5 | 366 | 0.59 | 0.76 | 33 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1167 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–A · 724 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 574 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 3F2D · DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mn and Zn · the same entry in another collection · chain P against P, 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 3F2D · PDBe 3F2D · UniProt Q5L0J3
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