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Crystal structure of the cytochrome B5 reductase domain of ulva prolifera nitrate reductase

Analyse Crystal structure of the cytochrome B5 reductase domain of ulva prolifera… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YLY
Type: protein
Length: 531 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrate reductase
Ligands: FAD
Pockets: 6 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrate reductase	protein	262	22% helix, 36% strand	—
B	Nitrate reductase	protein	269	21% helix, 36% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 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	434	0.63	0.77	48	FAD
2	411	0.60	0.76	49	FAD
3	191	0.46	0.74	31	empty
4	97	0.40	0.77	18	empty
5	64	0.36	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 405 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5YLY · Crystal structure of the cytochrome b5 reductase domain of Ulva prolifera nitrate… · 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
Elsewhere: RCSB PDB 5YLY · PDBe 5YLY

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