Complex 4qka

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	3.20
System mass	42.67 kDa
Deposition year	2014
Molecule type	RNA
# RNA entities	1
Organism	Thermoanaerobacter
RCSB PDB Entry	4qka
Reference	Gao Ang, Serganov Alexander. 2014. Structural insights into recognition of c-di-AMP by the ydaO riboswitch Nature Chemical Biology
Equivalence Class	NR_all_94866.4 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	2BA
Residue	. / 201
Chain	B / 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	574.53 Å³
Hydrophobicity	0.151
Hydrophilicity	0.965
Buriedness	0.709
Don/acc character	1.761
SiteScore	1.172
D Score	1.051
Kd	—

Pocket 2

Compound	2BA
Residue	. / 202
Chain	C / 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	306.99 Å³
Hydrophobicity	0.145
Hydrophilicity	0.975
Buriedness	0.701
Don/acc character	1.320
SiteScore	1.111
D Score	0.974
Kd	—