MolNFT v1 · #63195 · protein + DNA
DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp and mn
3F2C · Geobacillus kaustophilus DNA polc: “DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp and mn”. X-ray diffraction, 4 ligands (DGT, MN, ZN), 9 pockets (best druggability 0.75). MolNFT v1 #63195 on GenesisL1: 3D…
- PDB
- 3F2C
- Type
- protein + DNA
- Length
- 1,024 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geobacillus kaustophilus DNA polc; 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*D…
- EC
- 2.7.7.7
- UniProt
- Q5L0J3
- Ligands
- DGT, MN, ZN, SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geobacillus kaustophilus DNA polc (EC 2.7.7.7) | protein | 993 | 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
- MN · Manganese (II) ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.75 | 0.78 | 74 | empty |
| 2 | 720 | 0.74 | 0.80 | 89 | MN, SO4 |
| 3 | 532 | 0.69 | 0.79 | 47 | empty |
| 4 | 372 | 0.68 | 0.81 | 29 | MN, DGT |
| 5 | 361 | 0.58 | 0.75 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1150 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 724 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 579 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Compared structures
- 3F2C · DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP and Mn · 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 3F2C · PDBe 3F2C · UniProt Q5L0J3
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