MolNFT v1 · #87858 · protein
Crystal structure of M. mazei photolyase soaked with synthetic 8-hdf
4CDM · Deoxyribodipyrimidine photolyase: “Crystal structure of M. mazei photolyase soaked with synthetic 8-hdf”. X-ray diffraction, 3 ligands (FAD, FO1, SO4), 4 pockets (best druggability 0.83). MolNFT v1 #87858 on GenesisL1: 3D structure…
- PDB
- 4CDM
- Type
- protein
- Length
- 454 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribodipyrimidine photolyase
- EC
- 4.1.99.3
- UniProt
- Q8PYK9
- Ligands
- FAD, FO1, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribodipyrimidine photolyase (EC 4.1.99.3) | protein | 454 | 51% helix, 8% strand | Q8PYK9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains 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
- SO4 · Sulfate ion · ion · 4 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.83 | 0.88 | 49 | FAD, GOL |
| 2 | 421 | 0.80 | 0.88 | 37 | FO1 |
| 3 | 57 | 0.51 | 0.87 | 20 | SO4 |
| 4 | 121 | 0.44 | 0.77 | 22 | empty |
Compared structures
- 4CDM · Crystal structure of M. mazei photolyase soaked with synthetic 8-HDF · 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 Q8PYK9
- Elsewhere: RCSB PDB 4CDM · PDBe 4CDM · UniProt Q8PYK9
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