MolNFT v1 · #41165 · protein

3D structure of lumazine synthase from candida albicans

2JFB · 6,7-dimethyl-8-ribityllumazine synthase: “3D structure of lumazine synthase from candida albicans”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.75). MolNFT v1 #41165 on GenesisL1: 3D structure, binding sites…

PDB: 2JFB
Type: protein
Length: 2,291 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6,7-dimethyl-8-ribityllumazine synthase
EC: 2.5.1.9
Ligands: PO4
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, I, K, N, O	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9)	protein	153	49% helix, 19% strand	—
H, J, L, M	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9)	protein	152	51% helix, 18% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 15 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	620	0.75	0.82	52	PO4
2	790	0.72	0.77	49	MPD
3	714	0.71	0.78	48	MPD
4	705	0.71	0.78	48	MPD
5	550	0.71	0.80	53	PO4

Interfaces

25 interfaces between chains.

C–D · 1364 Å² buried · 17 hydrogen bonds · protein-protein
H–I · 1361 Å² buried · 13 hydrogen bonds · protein-protein
K–L · 1360 Å² buried · 14 hydrogen bonds · protein-protein
L–M · 1348 Å² buried · 16 hydrogen bonds · protein-protein
M–N · 1348 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2JFB · 3D Structure of Lumazine Synthase from Candida albicans · 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 2JFB · PDBe 2JFB

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