MolNFT v1 · #189518 · protein

Class II photolyase mmcpdii semiquinone to fully reduced tr-sfx studies (100 ns time-point)

7VJC · DNA photolyase: “Class II photolyase mmcpdii semiquinone to fully reduced tr-sfx studies (100 ns time-point)”. X-ray diffraction, 2 ligands (FAD, SO4), 4 pockets (best druggability 0.84). MolNFT v1 #189518 on GenesisL1: 3D…

PDB: 7VJC
Type: protein
Length: 453 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA photolyase
EC: 4.1.99.3
UniProt: Q8PYK9
Ligands: FAD, SO4
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA photolyase (EC 4.1.99.3)	protein	453	52% helix, 8% strand	Q8PYK9

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.84	0.90	42	FAD, DTT
2	349	0.79	0.89	38	empty
3	69	0.52	0.86	23	SO4
4	97	0.43	0.78	18	empty

Compared structures

7VJC · class II photolyase MmCPDII semiqui to fully reduced TR-SFX studies (100 ns time-point) · 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 7VJC · PDBe 7VJC · UniProt Q8PYK9

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