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Crystal structure of riboflavin lyase (rcae) with cofactor FMN

Analyse Crystal structure of riboflavin lyase (rcae) with cofactor FMN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W4Y
Type: protein
Length: 897 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Riboflavin lyase
Ligands: FMN
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Riboflavin lyase	protein	450	44% helix, 15% strand	—
B	Riboflavin lyase	protein	447	44% helix, 15% strand	—

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B

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

Pockets

9 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	783	0.76	0.80	70	FMN
2	680	0.72	0.79	61	FMN
3	327	0.57	0.76	40	empty
4	110	0.34	0.72	20	empty
5	89	0.33	0.74	24	empty

Interfaces

1 interface between chains.

A–B · 3398 Å² buried · 64 hydrogen bonds · protein-protein

Compared structures

5W4Y · Crystal Structure of Riboflavin Lyase (RcaE) with cofactor FMN · 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 5W4Y · PDBe 5W4Y

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