MolNFT v1 · #16168 · protein

Crystal structure of lumazine synthase from aquifex aeolicus in complex with inhibitor: 6,7-dioxo-5H-8-ribitylaminolumazine

1NQU · 6,7-dimethyl-8-ribityllumazine synthase: “Crystal structure of lumazine synthase from aquifex aeolicus in complex with inhibitor…”. X-ray diffraction, 2 ligands (RDL, PO4), 9 pockets (best druggability 0.74). MolNFT v1 #16168 on…

PDB: 1NQU
Type: protein
Length: 770 residues
Chains: 5
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: O66529
Ligands: RDL, PO4
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	154	50% helix, 24% strand	O66529

Ligands and binding sites

RDL · 6,7-dioxo-5H-8-ribitylaminolumazine · ligand · 5 copies · chains A, B, C, D, E
PO4 · Phosphate ion · ion · 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	634	0.74	0.81	33	empty
2	299	0.70	0.84	33	PO4, RDL
3	311	0.69	0.83	33	PO4, RDL
4	303	0.68	0.83	32	PO4, RDL
5	300	0.68	0.83	34	PO4, RDL

Interfaces

8 interfaces between chains.

B–C · 1518 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 1517 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1516 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1514 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1513 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1NQU · Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
O66529 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase (O66529) · 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 O66529
Elsewhere: RCSB PDB 1NQU · PDBe 1NQU · UniProt O66529

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