MolNFT v1 · #32842 · protein + DNA
Efficient and high fidelity incorporation of dctp opposite 7,8-dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase DPO4
2C2E · DNA polymerase IV: “Efficient and high fidelity incorporation of dctp opposite 7,8-dihydro-8-oxodeoxyguanosine by sulfolobus…”. X-ray diffraction, 2 ligands (DCP, CA), 3 pockets (best druggability 0.81). MolNFT v1 #32842 on…
- PDB
- 2C2E
- Type
- protein + DNA
- Length
- 370 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*C)-3'; 5'-D(*TP*CP*AP*C…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DCP, CA
- Pockets
- 3 · best druggability 0.81
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 | 341 | 42% helix, 24% strand | Q97W02 |
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*C)-3' | dna | 14 | — | — |
| T | 5'-D(*TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | dna | 15 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.81 | 0.82 | 91 | DCP, CA |
| 2 | 220 | 0.66 | 0.84 | 21 | empty |
| 3 | 120 | 0.47 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–T · 946 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–P · 710 Ų buried · 21 hydrogen bonds · protein-nucleic
- P–T · 635 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
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 Q97W02
- Elsewhere: RCSB PDB 2C2E · PDBe 2C2E · UniProt Q97W02
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