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Sfx structure of archaeal class II cpd photolyase from methanosarcina mazei in the fully reduced state

Analyse Sfx structure of archaeal class II cpd photolyase from methanosarcina mazei in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VJ7
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 · 53% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA photolyase (EC 4.1.99.3)	protein	453	53% 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	533	0.84	0.90	43	DTT, FAD
2	373	0.78	0.87	38	empty
3	76	0.48	0.83	20	SO4
4	92	0.43	0.79	19	empty

Compared structures

7VJ7 · SFX structure of archaeal class II CPD photolyase from Methanosarcina mazei in the fully… · 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 7VJ7 · PDBe 7VJ7 · UniProt Q8PYK9

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