Complex 9hmw

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	Electron Microscopy
Experimental resolution	2.25
System mass	3195.44 kDa
Deposition year	2024
Molecule type	RNA/Protein
# RNA entities	1
Organism	Arabidopsis
RCSB PDB Entry	9hmw
Reference	Ko Donghwi, Ruonala Raili, Faille Alexandre, Hellmann Eva, Help Hanna, Liu Huili, Nielsen Ronni, Haakonsson Anders, De Diego Nuria, Paatero Anja, Shcherbii Mariia V., Stefanowicz Karolina, Ćavar Zeljković Sanja, Drud Lundager Rasmussen Tine, Novak Ondrej, Bodi Zsuzsanna, Eswaran Gugan, Wybouw Brecht, Bourdon Matthieu, Urbez Cristina, Liu Xiaonan, Salokas Kari, Öhman Tiina, Waldie Tanya, Törönen Petri, el-Showk Sedeer, Balcerowicz Martin, Besnard Fabrice, Liu Xiaomin, Perkins Patrick, Mazzoni-Putman Serina, Vainonen Julia P., Sierla Maija, Frilander Mikko J., Mandrup Susanne, Vernoux Teva, Ljung Karin, Ferrando Alejandro, Blazquez Miguel A., Holm Liisa, Fray Rupert, Varjosalo Markku, Leyser Ottoline, Paavilainen Ville O., Mähönen Ari Pekka, Stepanova Anna, Alonso Jose, Heber Steffen, Malinowski Robert, Kirpekar Finn, Warren Alan J., Helariutta Ykä. 2026. Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate Science
Equivalence Class	NR_all_31124.2 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	EPE
Residue	. / 3404
Chain	OC / A
Non-redundant	True
Interacting RNA chains	B/A
RNA environment detailled	protein
RNA environment global	RNA/Protein
RNA family chains	B/A: rRNA
RNA family global	rRNA
Volume	633.86 Å³
Hydrophobicity	0.519
Hydrophilicity	1.157
Buriedness	0.796
Don/acc character	0.958
SiteScore	1.065
D Score	1.040
Kd	—

Pocket 2

Compound	TER
Residue	. / 3401
Chain	LC / A
Non-redundant	True
Interacting RNA chains	B/A
RNA environment detailled	protein, ion
RNA environment global	RNA/Protein
RNA family chains	B/A: rRNA
RNA family global	rRNA
Volume	873.96 Å³
Hydrophobicity	0.267
Hydrophilicity	1.628
Buriedness	0.883
Don/acc character	0.897
SiteScore	1.124
D Score	0.939
Kd	—