HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Complex 5d5l

System information

Experimental technique	X-ray
Experimental resolution	2.50
System mass	104.74 kDa
Deposition year	2015
Molecule type	RNA
# RNA entities	1
Organism	Lacticaseibacillus
RCSB PDB Entry	5d5l

Pocket 1

Compound	PRF
Residue	. / 117
Chain	U / A
Non-redundant	False
Interacting RNA chains	A/A
RNA environment detailled	RNA-only
RNA environment global	RNA
RNA family chains	A/A: riboswitch
RNA family global	riboswitch
Volume	98.10 Å³
Hydrophobicity	0.899
Hydrophilicity	0.946
Buriedness	0.644
Don/acc character	1.702
SiteScore	0.814
D Score	0.610
Kd	—

Pocket 2

Compound	PRF
Residue	. / 109
Chain	JA / B
Non-redundant	False
Interacting RNA chains	B/B
RNA environment detailled	RNA-only
RNA environment global	RNA
RNA family chains	B/B: riboswitch
RNA family global	riboswitch
Volume	99.47 Å³
Hydrophobicity	0.576
Hydrophilicity	0.845
Buriedness	0.604
Don/acc character	2.229
SiteScore	0.826
D Score	0.643
Kd	—

Pocket 3

Compound	PRF
Residue	. / 104
Chain	QA / C
Non-redundant	False
Interacting RNA chains	C/C
RNA environment detailled	RNA-only
RNA environment global	RNA
RNA family chains	C/C: riboswitch
RNA family global	riboswitch
Volume	87.81 Å³
Hydrophobicity	0.577
Hydrophilicity	0.936
Buriedness	0.616
Don/acc character	1.373
SiteScore	0.828
D Score	0.636
Kd	—

Pocket 4

Compound	PRF
Residue	. / 106
Chain	ZA / D
Non-redundant	False
Interacting RNA chains	D/D
RNA environment detailled	RNA-only
RNA environment global	RNA
RNA family chains	D/D: riboswitch
RNA family global	riboswitch
Volume	87.81 Å³
Hydrophobicity	0.705
Hydrophilicity	0.835
Buriedness	0.627
Don/acc character	2.007
SiteScore	0.811
D Score	0.619
Kd	—