HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 6ymj

System information

Experimental technique X-ray
Experimental resolution 2.04
System mass 71.02 kDa
Deposition year 2020
Molecule type RNA
# RNA entities 1
Organism Roseobacter
RCSB PDB Entry 6ymj
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
Equivalence Class NR_all_57046.3
BGSU version: 4.48

Compound ADN
Residue . / 201
Chain M / A
Non-redundant False
Interacting RNA chains B/B, A/A
RNA environment detailled other
RNA environment global RNA/Other
RNA family chains A/A: riboswitch, B/B: riboswitch
RNA family global riboswitch
Volume 353.63 Å3
Hydrophobicity 0.452
Hydrophilicity 1.056
Buriedness 0.705
Don/acc character 1.676
SiteScore 1.155
D Score 1.019
Kd —

Compound ADN
Residue . / 202
Chain N / A
Non-redundant False
Interacting RNA chains B/B, A/A
RNA environment detailled other
RNA environment global RNA/Other
RNA family chains A/A: riboswitch, B/B: riboswitch
RNA family global riboswitch
Volume 81.63 Å3
Hydrophobicity 0.373
Hydrophilicity 0.908
Buriedness 0.569
Don/acc character 4.086
SiteScore 0.744
D Score 0.543
Kd —

Compound ADN
Residue . / 102
Chain Q / C
Non-redundant False
Interacting RNA chains D/D, C/C
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/C: riboswitch, D/D: riboswitch
RNA family global riboswitch
Volume 431.84 Å3
Hydrophobicity 0.308
Hydrophilicity 0.979
Buriedness 0.644
Don/acc character 1.973
SiteScore 1.126
D Score 1.007
Kd —

Compound ADN
Residue . / 201
Chain S / F
Non-redundant False
Interacting RNA chains F/G, E/F
RNA environment detailled other
RNA environment global RNA/Other
RNA family chains E/F: riboswitch, F/G: riboswitch
RNA family global riboswitch
Volume 383.82 Å3
Hydrophobicity 0.447
Hydrophilicity 1.045
Buriedness 0.681
Don/acc character 1.851
SiteScore 1.139
D Score 1.008
Kd —

Compound ADN
Residue . / 202
Chain T / F
Non-redundant False
Interacting RNA chains F/G, E/F
RNA environment detailled other
RNA environment global RNA/Other
RNA family chains E/F: riboswitch, F/G: riboswitch
RNA family global riboswitch
Volume 74.09 Å3
Hydrophobicity 0.255
Hydrophilicity 0.935
Buriedness 0.551
Don/acc character 2.104
SiteScore 0.747
D Score 0.549
Kd —

Compound ADN
Residue . / 201
Chain U / I
Non-redundant False
Interacting RNA chains H/J, G/I
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains G/I: riboswitch, H/J: riboswitch
RNA family global riboswitch
Volume 373.18 Å3
Hydrophobicity 0.395
Hydrophilicity 1.021
Buriedness 0.684
Don/acc character 1.647
SiteScore 1.145
D Score 1.018
Kd —

Compound ADN
Residue . / 201
Chain V / M
Non-redundant False
Interacting RNA chains I/M, J/N
RNA environment detailled other
RNA environment global RNA/Other
RNA family chains I/M: riboswitch, J/N: riboswitch
RNA family global riboswitch
Volume 312.82 Å3
Hydrophobicity 0.270
Hydrophilicity 0.938
Buriedness 0.634
Don/acc character 2.052
SiteScore 1.127
D Score 1.015
Kd —

Compound ADN
Residue . / 101
Chain Y / N
Non-redundant False
Interacting RNA chains I/M, J/N
RNA environment detailled other
RNA environment global RNA/Other
RNA family chains I/M: riboswitch, J/N: riboswitch
RNA family global riboswitch
Volume 74.43 Å3
Hydrophobicity 0.284
Hydrophilicity 0.993
Buriedness 0.554
Don/acc character 1.946
SiteScore 0.725
D Score 0.515
Kd —

Compound ADN
Residue . / 102
Chain AA / O
Non-redundant False
Interacting RNA chains K/O, L/P
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains K/O: riboswitch, L/P: riboswitch
RNA family global riboswitch
Volume 323.45 Å3
Hydrophobicity 0.456
Hydrophilicity 1.067
Buriedness 0.695
Don/acc character 1.532
SiteScore 1.148
D Score 1.009
Kd —