MolNFT v1 · #60577 · protein + DNA
Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion and F0 cofactor
3CVV · DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DGP*DGP*(64T)P*(5PY)…: “Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion and F0 cofactor”. X-ray diffraction, 2 ligands (FAD, FO1), 9 pockets (best druggability…
- PDB
- 3CVV
- Type
- protein + DNA
- Length
- 549 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, FO1
- Pockets
- 9 · 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 | 519 | 51% helix, 7% strand | Q8SXK5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains C, A
- FO1 · 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol · ligand · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains C, D, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.86 | 0.96 | 34 | FAD |
| 2 | 259 | 0.77 | 0.89 | 39 | FO1 |
| 3 | 219 | 0.64 | 0.83 | 35 | empty |
| 4 | 83 | 0.47 | 0.82 | 14 | EDO |
| 5 | 106 | 0.43 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–A · 778 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 607 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- D–A · 504 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3CVV · Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion and… · 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 3CVV · PDBe 3CVV · UniProt Q8SXK5
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