MolNFT v1 · #29767 · protein

Recombinant lumazine synthase (hexagonal form)

1ZIS · 6,7-dimethyl-8-ribityllumazine synthase: “Recombinant lumazine synthase (hexagonal form)”. X-ray diffraction, 2 ligands (INI, PO4), 20 pockets (best druggability 0.76). MolNFT v1 #29767 on GenesisL1: 3D structure, binding sites and…

PDB: 1ZIS
Type: protein
Length: 1,540 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6,7-dimethyl-8-ribityllumazine synthase
EC: 2.5.1.78
UniProt: P11998
Ligands: INI, PO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	154	47% helix, 24% strand	P11998

Ligands and binding sites

INI · 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
PO4 · Phosphate ion · ion · 10 copies · chains A, E, B, C, D, F, J, G, H, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	729	0.76	0.81	63	empty
2	103	0.72	0.93	23	empty
3	108	0.71	0.93	23	empty
4	557	0.71	0.80	46	empty
5	115	0.71	0.92	22	empty

Interfaces

10 interfaces between chains.

A–E · 1431 Å² buried · 19 hydrogen bonds · protein-protein
F–J · 1428 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 1427 Å² buried · 19 hydrogen bonds · protein-protein
I–J · 1422 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1420 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

1ZIS · Recombinant Lumazine synthase (hexagonal form) · the same entry in another collection · chain J against J, TM-score 1.00
P11998 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase (P11998) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P11998
Elsewhere: RCSB PDB 1ZIS · PDBe 1ZIS · UniProt P11998

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