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Lumazine synthase from mycobacterium tuberculosis bound to N-6- (RIBITYLAMINO)PYRIMIDINE-2,4(1H,3H)-dione-5-yl-propionamide

Analyse Lumazine synthase from mycobacterium tuberculosis bound to N-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VI5
Type: protein
Length: 1,480 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6,7-dimethyl-8-ribityllumazine synthase
EC: 2.5.1.9
UniProt: P66034
Ligands: Y19, K, PO4
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9)	protein	150	48% helix, 19% strand	P66034
B, F, G	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9)	protein	147	49% helix, 20% strand	P66034
C, J	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9)	protein	146	49% helix, 21% strand	P66034
D, H	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9)	protein	148	49% helix, 20% strand	P66034
E	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9)	protein	151	48% helix, 20% strand	P66034

Ligands and binding sites

Y19 · 1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
K · Potassium ion · metal · 15 copies · chains A, J, B, I, C, H, D, G, E, F
PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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	803	0.78	0.82	55	empty
2	796	0.78	0.82	54	empty
3	251	0.77	0.90	36	Y19, PO4
4	247	0.76	0.89	31	Y19, PO4
5	265	0.75	0.88	31	Y19, PO4

Interfaces

25 interfaces between chains.

G–H · 1229 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1225 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 1207 Å² buried · 11 hydrogen bonds · protein-protein
I–J · 1205 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1196 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2VI5 · LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO… · 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
Every structure of UniProt P66034
Elsewhere: RCSB PDB 2VI5 · PDBe 2VI5 · UniProt P66034

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