Complex 8i3z

Legend

Pocket colors by molecule type

RNA

Protein

DNA

These colors appear when a pocket is selected (the structure fades to show the pocket surface). Colors from the molecule-type palette (RNA / protein / DNA).

System information

Experimental technique	X-ray
Experimental resolution	1.67
System mass	18.60 kDa
Deposition year	2023
Molecule type	RNA
# RNA entities	1
Organism	Streptococcus
RCSB PDB Entry	8i3z
Reference	Peng Xuemei, Liao Wenjian, Lin Xiaowei, Lilley David M J, Huang Lin. 2023. Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets Nucleic Acids Research
Equivalence Class	NR_all_83957.3 BGSU version: 4.52

Pockets List

Legend

Cell colors for SiteScore and D Score:

Favourable

Intermediate

Unfavourable

Not available

Score	Threshold	Meaning
SiteScore	< 0.8	Non-drug binding site
SiteScore	0.8 – 1.0	Potential drug binding site
SiteScore	> 1.0	Promising binding site
D Score	< 0.83	Undruggable
D Score	0.83 – 0.98	Difficult
D Score	> 0.98	Druggable

Tick a pocket below to highlight it in the 3D structure above.

Pocket 1

Compound	NMN
Residue	. / 101
Chain	D / B
Non-redundant	True
Interacting RNA chains	B/B, A/A
RNA environment detailled	RNA-only
RNA environment global	RNA
RNA family chains	A/A: riboswitch, B/B: riboswitch
RNA family global	riboswitch
Volume	165.33 Å³
Hydrophobicity	0.485
Hydrophilicity	0.973
Buriedness	0.689
Don/acc character	4.163
SiteScore	1.024
D Score	0.865
Kd	—

Pocket 2

Compound	NMN
Residue	. / 102
Chain	E / B
Non-redundant	False
Interacting RNA chains	B/B, A/A
RNA environment detailled	RNA-only
RNA environment global	RNA
RNA family chains	A/A: riboswitch, B/B: riboswitch
RNA family global	riboswitch
Volume	265.14 Å³
Hydrophobicity	0.103
Hydrophilicity	1.350
Buriedness	0.671
Don/acc character	1.510
SiteScore	1.132
D Score	0.902
Kd	—