Research workbench

T. thermophilus hibernating 70S ribosome

Analyse T. thermophilus hibernating 70S ribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GZQ
Type: protein + RNA
Length: 10,360 residues
Chains: 53
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.28
Source: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); Thermus thermophilus…
Molecule: 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S…
UniProt: P60405, Q5SHN8, Q5SHN9, Q5SHQ0, P0DOY8, Q5SLQ1, P60488, Q5SHP8, Q5SHQ7, P60489, Q9Z9H5, Q5SHQ4, P60490, P60491, P60492, Q5SHP3, Q5SHP0, Q5SHP9, Q5SHZ1, P60493, P60494, Q5SHP6, Q5SHQ6, Q5SJE1, P80339, P35871, P80340, Q5SKU1, Q5SHR2, P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, P0DOY9, P80374, Q5SHN7, P80376, Q5SHN3, P80377, P0DOY6, Q5SJ76, Q5SJH3, P0DOY7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3, Q5SIS0
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 3.28 · 53 distinct chains · 20% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C1	50S ribosomal protein L2	protein	272	4% helix, 19% strand	P60405
D1	50S ribosomal protein L3	protein	205	5% helix, 30% strand	Q5SHN8
E1	50S ribosomal protein L4	protein	208	22% helix, 9% strand	Q5SHN9
F1	50S ribosomal protein L5	protein	181	28% helix, 15% strand	Q5SHQ0
G1	50S ribosomal protein L6	protein	170	14% helix, 22% strand	P0DOY8
H1	50S ribosomal protein L9	protein	50	30% helix, 12% strand	Q5SLQ1
I1	50S ribosomal protein L13	protein	138	27% helix, 10% strand	P60488
J1	50S ribosomal protein L14	protein	122	5% helix, 37% strand	Q5SHP8
K1	50S ribosomal protein L15	protein	150	10% helix, 7% strand	Q5SHQ7
L1	50S ribosomal protein L16	protein	141	19% helix, 19% strand	P60489
M1	50S ribosomal protein L17	protein	117	33% helix, 18% strand	Q9Z9H5
N1	50S ribosomal protein L18	protein	111	27% helix, 19% strand	Q5SHQ4
O1	50S ribosomal protein L19	protein	137	12% helix, 34% strand	P60490
P1	50S ribosomal protein L20	protein	117	59% helix, 0% strand	P60491
Q1	50S ribosomal protein L21	protein	101	0% helix, 36% strand	P60492
R1	50S ribosomal protein L22	protein	113	30% helix, 29% strand	Q5SHP3
S1	50S ribosomal protein L23	protein	92	13% helix, 22% strand	Q5SHP0
T1	50S ribosomal protein L24	protein	102	0% helix, 27% strand	Q5SHP9
U1	50S ribosomal protein L25	protein	179	6% helix, 17% strand	Q5SHZ1
V1	50S ribosomal protein L27	protein	77	0% helix, 34% strand	P60493
W1	50S ribosomal protein L28	protein	97	7% helix, 29% strand	P60494
X1	50S ribosomal protein L29	protein	69	59% helix, 0% strand	Q5SHP6
Y1	50S ribosomal protein L30	protein	59	20% helix, 27% strand	Q5SHQ6
Z1	50S ribosomal protein L31	protein	63	0% helix, 0% strand	Q5SJE1
a1	50S ribosomal protein L32	protein	59	15% helix, 7% strand	P80339
b1	50S ribosomal protein L33	protein	45	0% helix, 27% strand	P35871
c1	50S ribosomal protein L34	protein	49	33% helix, 0% strand	P80340
d1	50S ribosomal protein L35	protein	61	11% helix, 7% strand	Q5SKU1
A1	23S ribosomal RNA	rna	2912	—	—
B1	5S ribosomal RNA	rna	122	—	—
e1	50S ribosomal protein L36	protein	36	8% helix, 31% strand	Q5SHR2
B2	30S ribosomal protein S2	protein	237	28% helix, 8% strand	P80371
C2	30S ribosomal protein S3	protein	206	18% helix, 29% strand	P80372
D2	30S ribosomal protein S4	protein	208	30% helix, 4% strand	P80373
E2	30S ribosomal protein S5	protein	151	27% helix, 32% strand	Q5SHQ5
F2	30S ribosomal protein S6	protein	101	17% helix, 32% strand	Q5SLP8
G2	30S ribosomal protein S7	protein	155	46% helix, 1% strand	P17291
H2	30S ribosomal protein S8	protein	138	23% helix, 29% strand	P0DOY9
I2	30S ribosomal protein S9	protein	127	17% helix, 17% strand	P80374
J2	30S ribosomal protein S10	protein	99	10% helix, 33% strand	Q5SHN7
K2	30S ribosomal protein S11	protein	118	18% helix, 25% strand	P80376
L2	30S ribosomal protein S12	protein	125	7% helix, 22% strand	Q5SHN3
M2	30S ribosomal protein S13	protein	117	27% helix, 0% strand	P80377
N2	30S ribosomal protein S14 type Z	protein	60	20% helix, 8% strand	P0DOY6
O2	30S ribosomal protein S15	protein	88	57% helix, 0% strand	Q5SJ76
P2	30S ribosomal protein S16	protein	84	13% helix, 31% strand	Q5SJH3
Q2	30S ribosomal protein S17	protein	100	12% helix, 35% strand	P0DOY7
R2	30S ribosomal protein S18	protein	62	37% helix, 6% strand	Q5SLQ0
S2	30S ribosomal protein S19	protein	78	5% helix, 14% strand	Q5SHP2
T2	30S ribosomal protein S20	protein	99	68% helix, 0% strand	P80380
U2	30S ribosomal protein Thx	protein	25	16% helix, 0% strand	Q5SIH3
V2	Ribosome hibernation promoting factor	protein	121	19% helix, 21% strand	Q5SIS0
A2	16S ribosomal RNA	rna	1506	—	—

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	784	0.88	0.93	76	empty
2	946	0.88	0.91	89	empty
3	1157	0.88	0.90	115	empty
4	1094	0.86	0.87	80	empty
5	614	0.85	0.91	58	empty

Interfaces

118 interfaces between chains.

C1–A1 · 7507 Å² buried · 110 hydrogen bonds · protein-nucleic
D1–A1 · 5088 Å² buried · 76 hydrogen bonds · protein-nucleic
K1–A1 · 5022 Å² buried · 86 hydrogen bonds · protein-nucleic
E1–A1 · 4340 Å² buried · 61 hydrogen bonds · protein-nucleic
P1–A1 · 4226 Å² buried · 53 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

P0DOY9 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (P0DOY9) · a predicted model of the same protein · chain H2 against A, TM-score 0.95
Q5SHR2 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L36 (Q5SHR2) · a predicted model of the same protein · chain e1 against A, TM-score 0.93
P0DOY8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L6 (P0DOY8) · a predicted model of the same protein · chain G1 against A, TM-score 0.92
P0DOY7 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S17 (P0DOY7) · a predicted model of the same protein · chain Q2 against A, TM-score 0.91
P0DOY6 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S14 type Z (P0DOY6) · a predicted model of the same protein · chain N2 against A, TM-score 0.86
Q5SLQ1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L9 (Q5SLQ1) · a predicted model of the same protein · chain H1 against A, TM-score 0.79

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