MolNFT v1 · #52782 · protein + DNA
Drosophila melanogaster (6-4) photolyase bound to double stranded DNA containing a T(6-4)C photolesion
2WB2: “Drosophila melanogaster (6-4) photolyase bound to double stranded DNA containing a T(6-4)C photolesion”. X-ray diffraction, 1 ligand (FAD), 10 pockets (best druggability 0.86). MolNFT v1 #52782 on GenesisL1: 3D structure, binding…
- PDB
- 2WB2
- Type
- protein + DNA
- Length
- 538 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photolyase; 5'-D(*AP*CP*AP*GP*CP*GP*GP*64PP*ZP*GP*CP*AP *GP*GP*T)-3'…
- EC
- 4.1.99.3
- UniProt
- Q8SXK5
- Ligands
- FAD
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photolyase (EC 4.1.99.3) | protein | 508 | 50% helix, 7% strand | Q8SXK5 |
| C | 5'-D(*AP*CP*AP*GP*CP*GP*GP*64PP*ZP*GP*CP*AP *GP*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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.86 | 0.96 | 34 | FAD |
| 2 | 526 | 0.77 | 0.84 | 36 | empty |
| 3 | 403 | 0.67 | 0.80 | 44 | empty |
| 4 | 182 | 0.50 | 0.77 | 25 | empty |
| 5 | 179 | 0.44 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 761 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 595 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–D · 461 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2WB2 · Drosophila Melanogaster (6-4) Photolyase Bound To double stranded Dna containing a… · 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 2WB2 · PDBe 2WB2 · UniProt Q8SXK5
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