HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 6ymi

System information

Experimental technique X-ray
Experimental resolution 2.50
System mass 72.85 kDa
Deposition year 2020
Molecule type RNA
# RNA entities 1
Organism Roseobacter
RCSB PDB Entry 6ymi
Reference Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. . Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research

Compound AMP
Residue . / 102
Chain Q / C
Non-redundant True
Interacting RNA chains D/D, J/N, C/C
Volume 439.04 Å3
Hydrophobicity 0.473
Hydrophilicity 1.105
Buriedness 0.668
Don/acc character 1.674
SiteScore 0.980
D Score 0.980

Compound AMP
Residue . / 102
Chain V / I
Non-redundant True
Interacting RNA chains H/J, G/I
Volume 394.45 Å3
Hydrophobicity 0.526
Hydrophilicity 1.036
Buriedness 0.716
Don/acc character 1.885
SiteScore 1.013
D Score 1.032

Compound AMP
Residue . / 201
Chain Z / O
Non-redundant True
Interacting RNA chains L/P, K/O
Volume 402.68 Å3
Hydrophobicity 0.412
Hydrophilicity 1.070
Buriedness 0.667
Don/acc character 1.687
SiteScore 0.979
D Score 0.991

Compound CBV
Residue . / 101
Chain P / C
Non-redundant False
Interacting RNA chains C/C
Volume 32.24 Å3
Hydrophobicity 0.243
Hydrophilicity 0.937
Buriedness 0.559
Don/acc character 0.691
SiteScore 0.530
D Score 0.461

Compound CBV
Residue . / 101
Chain U / I
Non-redundant True
Interacting RNA chains G/I
Volume 29.50 Å3
Hydrophobicity 0.370
Hydrophilicity 0.882
Buriedness 0.577
Don/acc character 0.483
SiteScore 0.448
D Score 0.356