Research workbench

Non-translating S. pombe ribosome

Analyse Non-translating S. pombe ribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 9AXT
Type: protein + RNA
Length: 15,732 residues
Chains: 75
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: Schizosaccharomyces pombe
Molecule: 18S ribosomal RNA; Small ribosomal subunit protein uS2A; Small ribosomal subunit protein…
UniProt: Q9Y7L8, O94438, O74892, O60128, Q9P4W9, O14277, Q9C0Z7, Q10101, Q9P7B2, O59675, O13614, P0CT73, O14062, P28189, P0CT57, Q9UTQ6, P0CT64, O42984, P0CT67, P58234, O74893, P05764, P0CT58, P0CT75, O13784, P79009, Q9UTG4, O74330, P0CT79, O74329, P0CT63, Q9UTI8, Q9HGL8, P0CT72, P40372, P35679, O74306, P79071, O60143, O13672, O74905, Q09127, P0CT77, O74175, O94238, Q9US22, O42848, O14339, Q8TFH1, O42699, P0CT68, O42706, Q09668, P0CT61, O74884, Q10330, P78946, O14388, P57728, Q92366, P52808, Q9URX6, P79015, Q9USX4, Q9URT8, O74904, O94658, P05733, Q9USR7, P05767, O14069
Ligands: ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 2.4 · 75 distinct chains · 33% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
AA	18S ribosomal RNA	rna	1705	—	—
AD	Small ribosomal subunit protein uS2A	protein	205	37% helix, 14% strand	Q9Y7L8
AE	Small ribosomal subunit protein eS1B	protein	216	31% helix, 33% strand	O94438
AF	Small ribosomal subunit protein uS5	protein	216	31% helix, 25% strand	O74892
AG	Small ribosomal subunit protein uS3	protein	216	34% helix, 20% strand	O60128
AH	Small ribosomal subunit protein eS4C	protein	261	15% helix, 29% strand	Q9P4W9
AI	Small ribosomal subunit protein uS7A	protein	203	48% helix, 5% strand	O14277
AJ	Small ribosomal subunit protein eS6B	protein	221	29% helix, 20% strand	Q9C0Z7
AK	Small ribosomal subunit protein eS7	protein	193	33% helix, 19% strand	Q10101
AL	Small ribosomal subunit protein eS8B	protein	188	28% helix, 29% strand	Q9P7B2
AM	Small ribosomal subunit protein uS4B	protein	178	51% helix, 4% strand	O59675
AN	Small ribosomal subunit protein eS10B	protein	92	38% helix, 14% strand	O13614
AO	Small ribosomal subunit protein uS17A	protein	143	3% helix, 37% strand	P0CT73
AP	Small ribosomal subunit protein eS12A	protein	121	40% helix, 7% strand	O14062
AQ	Small ribosomal subunit protein uS15	protein	150	57% helix, 0% strand	P28189
AR	Small ribosomal subunit protein uS11B	protein	128	23% helix, 24% strand	P0CT57
AS	Small ribosomal subunit protein uS19B	protein	119	30% helix, 8% strand	Q9UTQ6
AT	Small ribosomal subunit protein uS9A	protein	140	36% helix, 18% strand	P0CT64
AU	Small ribosomal subunit protein eS17A	protein	118	53% helix, 1% strand	O42984
AV	Small ribosomal subunit protein uS13B	protein	141	39% helix, 4% strand	P0CT67
AW	Small ribosomal subunit protein eS19A	protein	142	49% helix, 8% strand	P58234
Aa	Small ribosomal subunit protein uS10	protein	101	27% helix, 33% strand	O74893
Ab	Small ribosomal subunit protein eS21	protein	87	21% helix, 30% strand	P05764
Ac	Small ribosomal subunit protein uS8A	protein	129	34% helix, 27% strand	P0CT58
Ad	Small ribosomal subunit protein uS12A	protein	142	15% helix, 21% strand	P0CT75
Ae	Small ribosomal subunit protein eS24A	protein	133	37% helix, 29% strand	O13784
Af	Small ribosomal subunit protein eS25A	protein	69	43% helix, 13% strand	P79009
Ag	Small ribosomal subunit protein eS26B	protein	97	16% helix, 24% strand	Q9UTG4
Ah	Small ribosomal subunit protein eS27	protein	81	6% helix, 16% strand	O74330
Ai	Small ribosomal subunit protein eS28A	protein	63	0% helix, 46% strand	P0CT79
Aj	Small ribosomal subunit protein uS14	protein	53	25% helix, 9% strand	O74329
Ak	Small ribosomal subunit protein eS30B	protein	60	15% helix, 0% strand	P0CT63
B0	Large ribosomal subunit protein eL42	protein	93	11% helix, 38% strand	Q9UTI8
B1	Large ribosomal subunit protein eL43A	protein	93	41% helix, 14% strand	Q9HGL8
B2	28S ribosomal RNA	rna	3212	—	—
B3	5S ribosomal RNA	rna	119	—	—
B4	5.8S ribosomal RNA	rna	157	—	—
BN	Large ribosomal subunit protein uL2C	protein	248	11% helix, 27% strand	P0CT72
BO	Large ribosomal subunit protein uL3A	protein	384	17% helix, 28% strand	P40372
BP	Large ribosomal subunit protein uL4A	protein	362	34% helix, 10% strand	P35679
BQ	Large ribosomal subunit protein uL18B	protein	287	46% helix, 10% strand	O74306
BR	Large ribosomal subunit protein eL6	protein	162	19% helix, 15% strand	P79071
BS	Large ribosomal subunit protein uL30C	protein	233	55% helix, 15% strand	O60143
BT	Large ribosomal subunit protein eL8	protein	229	51% helix, 8% strand	O13672
BU	Large ribosomal subunit protein uL6B	protein	168	20% helix, 26% strand	O74905
BV	Large ribosomal subunit protein uL16A	protein	191	27% helix, 26% strand	Q09127
BW	Large ribosomal subunit protein uL5A	protein	167	28% helix, 23% strand	P0CT77
BX	Large ribosomal subunit protein eL13	protein	207	47% helix, 7% strand	O74175
BY	Large ribosomal subunit protein eL14	protein	130	45% helix, 23% strand	O94238
BZ	Large ribosomal subunit protein eL15B	protein	200	39% helix, 18% strand	Q9US22
Ba	Large ribosomal subunit protein uL13A	protein	196	53% helix, 12% strand	O42848
Bb	Large ribosomal subunit protein uL22A	protein	152	35% helix, 28% strand	O14339
Bc	Large ribosomal subunit protein eL18B	protein	186	32% helix, 18% strand	Q8TFH1
Bd	Large ribosomal subunit protein eL19B	protein	157	69% helix, 4% strand	O42699
Be	Large ribosomal subunit protein eL20A	protein	173	24% helix, 33% strand	P0CT68
Bf	Large ribosomal subunit protein eL21B	protein	159	21% helix, 21% strand	O42706
Bg	Large ribosomal subunit protein eL22	protein	99	31% helix, 24% strand	Q09668
Bh	Large ribosomal subunit protein uL14B	protein	134	9% helix, 32% strand	P0CT61
Bi	Large ribosomal subunit protein eL24B	protein	63	24% helix, 19% strand	O74884
Bj	Large ribosomal subunit protein uL23A	protein	118	25% helix, 17% strand	Q10330
Bk	Large ribosomal subunit protein uL24	protein	125	29% helix, 32% strand	P78946
Bl	Large ribosomal subunit protein eL27A	protein	135	26% helix, 24% strand	O14388
Bm	Large ribosomal subunit protein uL15B	protein	147	28% helix, 14% strand	P57728
Bn	Large ribosomal subunit protein eL29	protein	59	58% helix, 2% strand	Q92366
Bo	Large ribosomal subunit protein eL30A	protein	94	44% helix, 19% strand	P52808
Bp	Large ribosomal subunit protein eL31	protein	103	30% helix, 30% strand	Q9URX6
Bq	Large ribosomal subunit protein eL32A	protein	118	22% helix, 9% strand	P79015
Br	Large ribosomal subunit protein eL33A	protein	104	7% helix, 47% strand	Q9USX4
Bs	Large ribosomal subunit protein eL34B	protein	106	31% helix, 13% strand	Q9URT8
Bt	Large ribosomal subunit protein uL29	protein	121	67% helix, 2% strand	O74904
Bu	Large ribosomal subunit protein eL36B	protein	95	61% helix, 1% strand	O94658
Bv	Large ribosomal subunit protein eL37B	protein	82	26% helix, 7% strand	P05733
Bw	Large ribosomal subunit protein eL38A	protein	69	26% helix, 35% strand	Q9USR7
Bx	Large ribosomal subunit protein eL39	protein	50	34% helix, 0% strand	P05767
By	Large ribosomal subunit protein eL28	protein	134	35% helix, 18% strand	O14069

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains Ag, Ah, AA, Aj, B0, B1, Bv

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	941	0.89	0.92	92	empty
2	1031	0.88	0.90	114	empty
3	875	0.88	0.91	88	empty
4	986	0.88	0.90	77	empty
5	875	0.87	0.90	99	empty

Interfaces

226 interfaces between chains.

B2–BO · 8633 Å² buried · 201 hydrogen bonds · protein-nucleic
B2–BP · 8255 Å² buried · 168 hydrogen bonds · protein-nucleic
B2–BN · 7324 Å² buried · 186 hydrogen bonds · protein-nucleic
B2–BZ · 7124 Å² buried · 152 hydrogen bonds · protein-nucleic
B2–B4 · 5153 Å² buried · 268 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

P40372 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3-a (P40372) · a predicted model of the same protein · chain BO against A, TM-score 0.99
P0CT72 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L2-C (P0CT72) · a predicted model of the same protein · chain BN against A, TM-score 0.99
O74306 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L5-B (O74306) · a predicted model of the same protein · chain BQ against A, TM-score 0.99
Q9P4W9 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S4-C (Q9P4W9) · a predicted model of the same protein · chain AH against A, TM-score 0.99
O60143 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L7-C (O60143) · a predicted model of the same protein · chain BS against A, TM-score 0.99
Q9US22 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L15-B (Q9US22) · a predicted model of the same protein · chain BZ against A, TM-score 0.99
P0CT58 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S22-a (P0CT58) · a predicted model of the same protein · chain Ac against A, TM-score 0.99
O14339 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L17-a (O14339) · a predicted model of the same protein · chain Bb against A, TM-score 0.99
Q9URX6 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L31 (Q9URX6) · a predicted model of the same protein · chain Bp against A, TM-score 0.99
O42699 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L19-B (O42699) · a predicted model of the same protein · chain Bd against A, TM-score 0.99
P78946 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26 (P78946) · a predicted model of the same protein · chain Bk against A, TM-score 0.99
O74892 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S2 (O74892) · a predicted model of the same protein · chain AF against A, TM-score 0.98

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.