Research workbench
Eukaryotic class II cpd photolyase structure reveals a basis for improved UV-tolerance in plants
Analyse Eukaryotic class II cpd photolyase structure reveals a basis for improved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UMV
- Type
- protein
- Length
- 940 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribodipyrimidine photo-lyase
- EC
- 4.1.99.3
- UniProt
- Q6F6A2
- Ligands
- URE, FAD
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribodipyrimidine photo-lyase (EC 4.1.99.3) | protein | 472 | 54% helix, 7% strand | Q6F6A2 |
| B | Deoxyribodipyrimidine photo-lyase (EC 4.1.99.3) | protein | 468 | 54% helix, 7% strand | Q6F6A2 |
Ligands and binding sites
- URE · Urea · ligand · 9 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.84 | 0.89 | 42 | FAD |
| 2 | 633 | 0.83 | 0.87 | 51 | FAD |
| 3 | 91 | 0.78 | 0.99 | 21 | EDO, URE |
| 4 | 97 | 0.78 | 0.98 | 21 | URE |
| 5 | 196 | 0.53 | 0.78 | 24 | URE |
Compared structures
- 3UMV · Eukaryotic Class II CPD photolyase structure reveals a basis for improved UV-tolerance in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6F6A2 · AlphaFold monomer V2.0 prediction for deoxyribodipyrimidine photo- lyase (Q6F6A2) · a predicted model of the same protein · 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 Q6F6A2
- Elsewhere: RCSB PDB 3UMV · PDBe 3UMV · UniProt Q6F6A2
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