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class II photolyase MmCPDII oxidized to semiqui TR-SFX studies (10 us time-point)

Analyse class II photolyase MmCPDII oxidized to semiqui TR-SFX studies (10 us… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VJ1
Type: protein
Length: 450 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.25
Source: Methanosarcina mazei Go1
Molecule: DNA photolyase
EC: 4.1.99.3
UniProt: Q8PYK9
Ligands: FAD, SO4
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · resolution 2.25 · 1 distinct chain · 51% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA photolyase (EC 4.1.99.3)	protein	450	51% helix, 7% strand	Q8PYK9

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
SO4 · Sulfate ion · ion · 3 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	559	0.84	0.89	47	SO4, FAD
2	383	0.81	0.90	42	empty
3	122	0.43	0.76	23	empty
4	78	0.40	0.78	16	empty

Compared structures

7VJ1 · Class II photolyase mmcpdii oxidized to semiquinone tr-sfx studies (10 us 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 7VJ1 · PDBe 7VJ1 · UniProt Q8PYK9

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