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Class II photolyase mmcpdii semiquinone to fully reduced tr-sfx studies (10 ns time-point)

Analyse Class II photolyase mmcpdii semiquinone to fully reduced tr-sfx studies (10 ns… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VJA
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 · 51% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA photolyase (EC 4.1.99.3)	protein	453	51% 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	558	0.84	0.90	45	FAD, DTT
2	375	0.78	0.87	47	empty
3	82	0.53	0.85	22	SO4
4	102	0.42	0.78	23	empty

Compared structures

7VJA · class II photolyase MmCPDII semiqui to fully reduced TR-SFX studies (10 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 7VJA · PDBe 7VJA · UniProt Q8PYK9

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