Research workbench
Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion
Analyse Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CVU
- Type
- protein + DNA
- Length
- 531 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DGP*DGP*(64T)P*(5PY) P*DGP*DCP*DAP*DGP*DGP*DT)-3'); DNA…
- UniProt
- Q8SXK5
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DGP*DGP*(64T)P*(5PY) P*DGP*DCP*DAP*DGP*DGP*DT)-3') | dna | 15 | — | — |
| D | DNA (5'- D(*DTP*DAP*DCP*DCP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DTP*DG)-3') | dna | 15 | — | — |
| A | RE11660P | protein | 501 | 51% helix, 7% strand | Q8SXK5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.86 | 0.96 | 34 | FAD |
| 2 | 515 | 0.76 | 0.83 | 40 | empty |
| 3 | 271 | 0.64 | 0.81 | 33 | empty |
| 4 | 239 | 0.52 | 0.76 | 34 | empty |
| 5 | 127 | 0.43 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–A · 755 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 604 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- D–A · 451 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3CVU · Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion · the same entry in another collection · chain C against C, 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 Q8SXK5
- Elsewhere: RCSB PDB 3CVU · PDBe 3CVU · UniProt Q8SXK5
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