Research workbench

Lumazine synthase from mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-YL)HEXANE 1-phosphate

Analyse Lumazine synthase from mycobacterium tuberculosis bound to 3-(1,3,7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2C9D
Type: protein
Length: 1,466 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: PHR, K
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).

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

Ligands and binding sites

PHR · 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl ) hexane 1-phosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
K · Potassium ion · metal · 17 copies · chains A, H, B, D, J, G, C, F, E, I
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	892	0.83	0.85	98	K
2	846	0.82	0.85	89	K
3	971	0.79	0.81	54	MPD
4	438	0.78	0.86	50	PHR
5	894	0.78	0.81	54	MPD

Interfaces

25 interfaces between chains.

G–H · 1211 Å² buried · 8 hydrogen bonds · protein-protein
I–J · 1189 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1173 Å² buried · 6 hydrogen bonds · protein-protein
F–J · 1167 Å² buried · 8 hydrogen bonds · protein-protein
H–I · 1167 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2C9D · Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3,7… · 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 2C9D · PDBe 2C9D · UniProt P66034

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.