MolNFT v1 · #137951 · protein

Crystal structure of riboflavin lyase (rcae)

5W48: “Crystal structure of riboflavin lyase (rcae)”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.75). MolNFT v1 #137951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5W48
Type: protein
Length: 900 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Riboflavin lyase
Ligands: SO4
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Riboflavin lyase	protein	452	42% helix, 15% strand	—
B	Riboflavin lyase	protein	448	40% helix, 15% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 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	1060	0.75	0.78	108	SO4
2	729	0.74	0.80	59	SO4
3	55	0.34	0.77	16	empty
4	61	0.32	0.76	16	empty
5	64	0.26	0.72	13	empty

Interfaces

1 interface between chains.

A–B · 3388 Å² buried · 60 hydrogen bonds · protein-protein

Compared structures

5W48 · Crystal Structure of Riboflavin Lyase (RcaE) · 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 5W48 · PDBe 5W48

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.