MolNFT v1 · #129035 · protein

Mutant of class II cpd photolyase from methanosarcina mazei - Y345F

5O8D · Deoxyribodipyrimidine photolyase: “Mutant of class II cpd photolyase from methanosarcina mazei - Y345F”. X-ray diffraction, 2 ligands (FAD, SO4), 5 pockets (best druggability 0.84). MolNFT v1 #129035 on GenesisL1: 3D structure…

PDB: 5O8D
Type: protein
Length: 451 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, SO4
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyribodipyrimidine photolyase (EC 4.1.99.3)	protein	451	53% helix, 8% strand	Q8PYK9

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
SO4 · Sulfate ion · ion · 8 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

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.84	0.89	43	FAD, GOL
2	357	0.78	0.87	46	SO4, GOL
3	69	0.51	0.85	20	SO4
4	114	0.44	0.78	22	empty
5	107	0.42	0.77	26	empty

Compared structures

5O8D · Mutant of class II CPD photolyase from Methanosarcina mazei - Y345F · 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 5O8D · PDBe 5O8D · UniProt Q8PYK9

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