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Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(6-4)C lesion
Analyse Structure of the 6-4 photolyase of D. melanogaster in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WQ7
- Type
- protein + DNA
- Length
- 538 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RE11660P; 5'-D(*AP*CP*AP*GP*CP*GP*GP*TDYP*ZP*GP* CP*AP*AP*GP*T)-3'…
- EC
- 4.1.99.3
- UniProt
- Q8SXK5
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RE11660P (EC 4.1.99.3) | protein | 508 | 50% helix, 7% strand | Q8SXK5 |
| C | 5'-D(*AP*CP*AP*GP*CP*GP*GP*TDYP*ZP*GP* CP*AP*AP*GP*T)-3' | dna | 15 | — | — |
| D | 5'-D(*TP*AP*CP*CP*TP*GP*CP*GP*AP*CP* CP*GP*CP*TP*G)-3' | dna | 15 | — | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
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 | 304 | 0.85 | 0.95 | 34 | FAD |
| 2 | 587 | 0.80 | 0.85 | 39 | empty |
| 3 | 280 | 0.64 | 0.81 | 37 | empty |
| 4 | 252 | 0.51 | 0.75 | 31 | empty |
| 5 | 184 | 0.42 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 773 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 601 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–D · 443 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2WQ7 · Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural… · 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 Q8SXK5
- Elsewhere: RCSB PDB 2WQ7 · PDBe 2WQ7 · UniProt Q8SXK5
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