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Hibernating ribosome from Staphylococcus aureus (Rotated state)

Analyse Hibernating ribosome from Staphylococcus aureus (Rotated state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ND9
Type: protein + RNA
Length: 10,030 residues
Chains: 52
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.7
Source: Staphylococcus aureus (strain NCTC 8325); Staphylococcus aureus subsp. aureus…
Molecule: 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
UniProt: Q2FZ25, Q2FW12, Q2FXK6, Q2FW23, Q2G113, P48940, Q2FW20, Q2FW39, Q931G5, Q2FW31, P0A0H0, Q2FW30, Q2FW19, Q2G2Q1, Q2FZ45, Q2FW15, Q2G111, Q2FW10, Q2FXY6, Q2FXZ7, Q2G055, P60430, Q2FW06, Q2FW07, Q2FW18, Q2FW21, Q2FW38, Q2FW16, P0A0F8, Q2FW13, Q2FW33, Q2FW22, Q2FZ42, Q2FXQ1, Q2FXS8, Q2FW11, Q2FW08, Q2FW17, Q2G0S0, Q2FXT0, Q2FZ60, Q2FW14, P0A0G2, Q2FWD8, Q2FZF1, Q2FY22, Q2FUQ0, Q2FXQ0, Q2FW29
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 3.7 · 52 distinct chains · 26% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	16S ribosomal RNA	rna	1541	—	—
b	30S ribosomal protein S2	protein	222	50% helix, 5% strand	Q2FZ25
c	30S ribosomal protein S3	protein	203	33% helix, 13% strand	Q2FW12
d	30S ribosomal protein S4	protein	197	39% helix, 6% strand	Q2FXK6
e	30S ribosomal protein S5	protein	160	24% helix, 21% strand	Q2FW23
f	30S ribosomal protein S6	protein	94	24% helix, 36% strand	Q2G113
g	30S ribosomal protein S7	protein	143	58% helix, 6% strand	P48940
h	30S ribosomal protein S8	protein	131	27% helix, 18% strand	Q2FW20
i	30S ribosomal protein S9	protein	128	25% helix, 19% strand	Q2FW39
j	30S ribosomal protein S10	protein	99	24% helix, 32% strand	Q931G5
k	30S ribosomal protein S11	protein	115	26% helix, 28% strand	Q2FW31
l	30S ribosomal protein S12	protein	135	4% helix, 17% strand	P0A0H0
m	30S ribosomal protein S13	protein	110	35% helix, 0% strand	Q2FW30
n	30S ribosomal protein S14 type Z	protein	60	28% helix, 3% strand	Q2FW19
o	30S ribosomal protein S15	protein	88	74% helix, 0% strand	Q2G2Q1
p	30S ribosomal protein S16	protein	90	24% helix, 17% strand	Q2FZ45
q	30S ribosomal protein S17	protein	85	0% helix, 33% strand	Q2FW15
r	30S ribosomal protein S18	protein	56	48% helix, 0% strand	Q2G111
s	30S ribosomal protein S19	protein	84	8% helix, 8% strand	Q2FW10
t	30S ribosomal protein S20	protein	80	75% helix, 0% strand	Q2FXY6
u	30S ribosomal protein S21	protein	45	62% helix, 0% strand	Q2FXZ7
v	Ribosome hibernation promotion factor	protein	101	34% helix, 16% strand	Q2G055
A	23S ribosomal RNA	rna	2914	—	—
B	5S ribosomal RNA	rna	114	—	—
D	50S ribosomal protein L2	protein	275	3% helix, 19% strand	P60430
E	50S ribosomal protein L3	protein	218	5% helix, 27% strand	Q2FW06
F	50S ribosomal protein L4	protein	199	27% helix, 6% strand	Q2FW07
G	50S ribosomal protein L5	protein	166	25% helix, 7% strand	Q2FW18
H	50S ribosomal protein L6	protein	164	21% helix, 24% strand	Q2FW21
M	50S ribosomal protein L13	protein	145	22% helix, 15% strand	Q2FW38
N	50S ribosomal protein L14	protein	122	6% helix, 20% strand	Q2FW16
O	50S ribosomal protein L15	protein	131	7% helix, 0% strand	P0A0F8
P	50S ribosomal protein L16	protein	133	18% helix, 21% strand	Q2FW13
Q	50S ribosomal protein L17	protein	117	40% helix, 10% strand	Q2FW33
R	50S ribosomal protein L18	protein	119	35% helix, 14% strand	Q2FW22
S	50S ribosomal protein L19	protein	107	9% helix, 33% strand	Q2FZ42
T	50S ribosomal protein L20	protein	116	71% helix, 0% strand	Q2FXQ1
U	50S ribosomal protein L21	protein	102	0% helix, 38% strand	Q2FXS8
V	50S ribosomal protein L22	protein	112	34% helix, 34% strand	Q2FW11
W	50S ribosomal protein L23	protein	89	25% helix, 27% strand	Q2FW08
X	50S ribosomal protein L24	protein	87	0% helix, 23% strand	Q2FW17
Y	50S ribosomal protein L25	protein	94	18% helix, 31% strand	Q2G0S0
Z	50S ribosomal protein L27	protein	77	0% helix, 26% strand	Q2FXT0
0	50S ribosomal protein L28	protein	46	0% helix, 26% strand	Q2FZ60
1	50S ribosomal protein L29	protein	65	72% helix, 0% strand	Q2FW14
2	50S ribosomal protein L30	protein	57	30% helix, 25% strand	P0A0G2
3	50S ribosomal protein L31 type B	protein	81	0% helix, 5% strand	Q2FWD8
4	50S ribosomal protein L32	protein	44	14% helix, 9% strand	Q2FZF1
5	50S ribosomal protein L33 2	protein	28	0% helix, 0% strand	Q2FY22
6	50S ribosomal protein L34	protein	44	48% helix, 0% strand	Q2FUQ0
7	50S ribosomal protein L35	protein	60	5% helix, 3% strand	Q2FXQ0
8	50S ribosomal protein L36	protein	37	8% helix, 19% strand	Q2FW29

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.88	0.90	123	empty
2	1122	0.88	0.90	103	empty
3	1106	0.86	0.89	100	empty
4	1092	0.86	0.88	100	empty
5	431	0.86	0.95	56	empty

Interfaces

111 interfaces between chains.

A–D · 7100 Å² buried · 132 hydrogen bonds · protein-nucleic
A–E · 5227 Å² buried · 97 hydrogen bonds · protein-nucleic
A–F · 4270 Å² buried · 88 hydrogen bonds · protein-nucleic
A–O · 4106 Å² buried · 69 hydrogen bonds · protein-nucleic
A–T · 3992 Å² buried · 84 hydrogen bonds · protein-nucleic

Compared structures

P60430 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P60430) · a predicted model of the same protein · chain D against A, TM-score 0.97
Q2FW38 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (Q2FW38) · a predicted model of the same protein · chain M against A, TM-score 0.96
Q2FW11 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (Q2FW11) · a predicted model of the same protein · chain V against A, TM-score 0.96
Q2FW07 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (Q2FW07) · a predicted model of the same protein · chain F against A, TM-score 0.95
Q2FXQ1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (Q2FXQ1) · a predicted model of the same protein · chain T against A, TM-score 0.95
Q2FW16 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L14 (Q2FW16) · a predicted model of the same protein · chain N against A, TM-score 0.95
Q2FZ25 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S2 (Q2FZ25) · a predicted model of the same protein · chain b against A, TM-score 0.95
Q2FW13 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (Q2FW13) · a predicted model of the same protein · chain P against A, TM-score 0.95
Q2FW12 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (Q2FW12) · a predicted model of the same protein · chain c against A, TM-score 0.95
Q2FW20 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (Q2FW20) · a predicted model of the same protein · chain h against A, TM-score 0.95
Q2FW33 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L17 (Q2FW33) · a predicted model of the same protein · chain Q against A, TM-score 0.94
Q2FXS8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L21 (Q2FXS8) · a predicted model of the same protein · chain U against A, TM-score 0.94

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