Research workbench

Lumazine synthase from saccharomyces cerevisiae

Analyse Lumazine synthase from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EJB
Type: protein
Length: 840 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lumazine synthase
EC: 2.5.1.78
UniProt: P50861
Ligands: INJ
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Lumazine synthase (EC 2.5.1.78)	protein	168	48% helix, 16% strand	P50861

Ligands and binding sites

INJ · 5-(6-D-ribitylamino-2,4-dihydroxypyrimidin-5-yl)-1-pentyl-phosphonic acid · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1081	0.80	0.81	75	empty
2	361	0.80	0.89	43	INJ
3	387	0.74	0.84	47	INJ
4	329	0.72	0.85	35	INJ
5	241	0.71	0.86	31	INJ

Interfaces

5 interfaces between chains.

C–D · 1777 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1635 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1537 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1531 Å² buried · 23 hydrogen bonds · protein-protein
A–E · 1416 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1EJB · Lumazine synthase from saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
P50861 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase (P50861) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P50861
Elsewhere: RCSB PDB 1EJB · PDBe 1EJB · UniProt P50861

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