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Yeast 80S ribosome.

Analyse Yeast 80S ribosome. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4V7R
Type: protein + RNA
Length: 26,657 residues
Chains: 139
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4
Source: Saccharomyces cerevisiae; Saccharomyces cerevisiae S288c
Molecule: 18S ribosomal RNA; 40S ribosomal protein S0-A; 40S ribosomal protein S2; 40S ribosomal…
UniProt: P32905, P25443, P05750, P26783, O13516, P26781, P05756, P06367, Q01855, P40213, P02407, P35271, P07280, P38701, P0C0W1, P32827, Q3E792, Q3E7X9, P41057, P38011, P53030, P05736, P14126, P10664, P26321, Q02326, P05737, P17076, P05738, P41805, P0C0W9, P36105, P05748, P26784, P05740, P07279, P05735, Q02753, P04451, P04449, P04456, P05743, P02406, P14120, P0C2H8, P38061, P39741, P49166, P04650, P02405, P49631, P17079, P05317
Ligands: OHX
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · resolution 4 · 74 distinct chains · 21% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A1, C1	18S ribosomal RNA	rna	1789	—	—
AA, CA	40S ribosomal protein S0-A	protein	220	25% helix, 3% strand	P32905
AB, CB	40S ribosomal protein S2	protein	219	16% helix, 11% strand	P25443
AC, CC	40S ribosomal protein S3	protein	189	29% helix, 12% strand	P05750
AD, CD	40S ribosomal protein S5	protein	169	34% helix, 1% strand	P26783
AE, CE	40S ribosomal protein S9-A	protein	157	36% helix, 1% strand	O13516
AF, CF	40S ribosomal protein S11	protein	77	0% helix, 6% strand	P26781
AG, CG	40S ribosomal protein S13	protein	117	38% helix, 2% strand	P05756
AH, CH	40S ribosomal protein S14-A	protein	128	11% helix, 5% strand	P06367
AI, CI	40S ribosomal protein S15	protein	121	8% helix, 5% strand	Q01855
AJ, CJ	40S ribosomal protein S16	protein	134	15% helix, 4% strand	P40213
AK, CK	40S ribosomal protein S17-A	protein	67	28% helix, 0% strand	P02407
AL, CL	40S ribosomal protein S18	protein	120	32% helix, 0% strand	P35271
AM, CM	40S ribosomal protein S19-A	protein	106	25% helix, 0% strand	P07280
AN, CN	40S ribosomal protein S20	protein	111	7% helix, 20% strand	P38701
AO, CO	40S ribosomal protein S22-A	protein	127	26% helix, 5% strand	P0C0W1
AP, CP	40S ribosomal protein S23	protein	116	0% helix, 12% strand	P32827
AQ	40S ribosomal protein S25-A	protein	67	27% helix, 0% strand	Q3E792
AR, CR	40S ribosomal protein S28-A	protein	47	0% helix, 0% strand	Q3E7X9
AS, CS	40S ribosomal protein S29-A	protein	39	8% helix, 0% strand	P41057
AT, CT	Guanine nucleotide-binding protein subunit beta-like protein; RACK-1	protein	313	0% helix, 30% strand	P38011
Aa, Bo, Ca	Unassigned secondary structure	protein	20	70% helix, 0% strand	—
Ab, Cb	Unassigned secondary structure	protein	105	18% helix, 0% strand	—
Ac, Cc	Unassigned secondary structure	protein	93	24% helix, 4% strand	—
Ad, Cd	Unassigned secondary structure	protein	35	20% helix, 0% strand	—
Ae, Bj, Dj	Unassigned secondary structure	protein	21	71% helix, 0% strand	—
Af	Unassigned secondary structure	protein	11	0% helix, 0% strand	—
Ah, Ch	Unassigned secondary structure	protein	41	68% helix, 0% strand	—
B1, D1	25S ribosomal RNA	rna	3206	—	—
B2, D2	5S ribosomal RNA	rna	121	—	—
B3, D3	5.8S ribosomal RNA	rna	158	—	—
BA, DA	60S ribosomal protein L1	protein	213	14% helix, 0% strand	P53030
BB, DB	60S ribosomal protein L2	protein	234	1% helix, 8% strand	P05736
BC, DC	60S ribosomal protein L3	protein	364	5% helix, 3% strand	P14126
BD, DD	60S ribosomal protein L4-A	protein	268	22% helix, 2% strand	P10664
BE, DE	60S ribosomal protein L5	protein	287	14% helix, 3% strand	P26321
BF, DF	60S ribosomal protein L6-A	protein	176	13% helix, 2% strand	Q02326
BG, DG	60S ribosomal protein L7-A	protein	215	41% helix, 0% strand	P05737
BH, DH	60S ribosomal protein L8-A	protein	173	34% helix, 1% strand	P17076
BI, DI	60S ribosomal protein L9-A	protein	191	19% helix, 16% strand	P05738
BJ, DJ	60S ribosomal protein L10	protein	208	24% helix, 12% strand	P41805
BK, DK	60S ribosomal protein L11-A	protein	165	13% helix, 4% strand	P0C0W9
BN, DN	60S ribosomal protein L14-A	protein	120	30% helix, 0% strand	P36105
BO, DO	60S ribosomal protein L15-A	protein	187	20% helix, 6% strand	P05748
BP, DP	60S ribosomal protein L16-A	protein	196	42% helix, 0% strand	P26784
BQ, DQ	60S ribosomal protein L17-A	protein	154	27% helix, 4% strand	P05740
BR, DR	60S ribosomal protein L18	protein	143	29% helix, 1% strand	P07279
BS, DS	60S ribosomal protein L19	protein	188	63% helix, 2% strand	P05735
BT, DT	60S ribosomal protein L21-A	protein	119	14% helix, 2% strand	Q02753
BU, DU	60S ribosomal protein L23	protein	129	9% helix, 20% strand	P04451
BV, DV	60S ribosomal protein L24-A	protein	59	12% helix, 7% strand	P04449
BW, DW	60S ribosomal protein L25	protein	94	23% helix, 0% strand	P04456
BX, DX	60S ribosomal protein L26-A	protein	107	15% helix, 22% strand	P05743
BY, DY	60S ribosomal protein L28	protein	149	9% helix, 6% strand	P02406
BZ, DZ	60S ribosomal protein L30	protein	98	37% helix, 2% strand	P14120
Ba, Da	60S ribosomal protein L31-A	protein	86	20% helix, 0% strand	P0C2H8
Bb, Db	60S ribosomal protein L32	protein	125	19% helix, 3% strand	P38061
Bc, Dc	60S ribosomal protein L35	protein	68	56% helix, 0% strand	P39741
Bd, Dd	60S ribosomal protein L37-A	protein	72	0% helix, 3% strand	P49166
Be, De	60S ribosomal protein L39	protein	48	31% helix, 0% strand	P04650
Bf, Df	60S ribosomal protein L42	protein	95	6% helix, 11% strand	P02405
Bg, Dg	60S ribosomal protein L43	protein	83	27% helix, 6% strand	P49631
Bh, Dh	Unassigned secondary structure	protein	44	50% helix, 0% strand	—
Bi, Di	Unassigned secondary structure	protein	12	0% helix, 0% strand	—
Bk, Dk	Unassigned secondary structure	protein	16	75% helix, 0% strand	—
Bl	Unassigned secondary structure	protein	19	42% helix, 0% strand	—
Bm	Unassigned secondary structure	protein	9	78% helix, 0% strand	—
Bn	Unassigned secondary structure	protein	27	44% helix, 0% strand	—
Bp	Unassigned secondary structure	protein	8	0% helix, 0% strand	—
Bq	Unassigned secondary structure	protein	17	82% helix, 0% strand	—
Br	Unassigned secondary structure	protein	23	65% helix, 0% strand	—
CQ	40S ribosomal protein S25-A	protein	63	21% helix, 0% strand	Q3E792
DL	60S ribosomal protein L12	protein	138	14% helix, 1% strand	P17079
DM	60S acidic ribosomal protein P0	protein	130	21% helix, 5% strand	P05317

Ligands and binding sites

OHX · osmium (III) hexammine · ligand · 715 copies · chains A1, AB, AP, Ae, B1, AN, AI, AL, AS, AT, Ac, Bd, BO, B3, Bf, BJ, BP, BY, BS, BG, BC, B2, Bb, BB, BF, BT, Bg, C1, D1, DU, CN, CL, CP, CI, CS, CT, Dd, DD, DO, D3, Df, DY, DS, DJ, DP, DC, DG, De, Db, D2, DN, DF, DE, DT, Dg

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	1631	0.88	0.91	137	OHX
2	2000	0.88	0.91	176	OHX
3	977	0.88	0.91	105	empty
4	869	0.88	0.92	73	OHX
5	1227	0.88	0.90	88	OHX

Interfaces

271 interfaces between chains.

D1–D3 · 5123 Å² buried · 303 hydrogen bonds · nucleic-nucleic
B1–B3 · 5086 Å² buried · 316 hydrogen bonds · nucleic-nucleic
D1–DC · 4695 Å² buried · 78 hydrogen bonds · protein-nucleic
B1–BC · 4679 Å² buried · 76 hydrogen bonds · protein-nucleic
B1–BB · 4208 Å² buried · 79 hydrogen bonds · protein-nucleic

Compared structures

P38011 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit… · a predicted model of the same protein · chain CT against A, TM-score 0.97
P10664 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L4-a (P10664) · a predicted model of the same protein · chain BD against A, TM-score 0.95
P05743 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26-a (P05743) · a predicted model of the same protein · chain BX against A, TM-score 0.94
P05737 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L7-a (P05737) · a predicted model of the same protein · chain BG against A, TM-score 0.94
P26784 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L16-a (P26784) · a predicted model of the same protein · chain BP against A, TM-score 0.94
P05738 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L9-a (P05738) · a predicted model of the same protein · chain BI against A, TM-score 0.93
P05750 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S3 (P05750) · a predicted model of the same protein · chain AC against A, TM-score 0.93
P05740 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L17-a (P05740) · a predicted model of the same protein · chain BQ against A, TM-score 0.93
P05748 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L15-a (P05748) · a predicted model of the same protein · chain BO against A, TM-score 0.92
Q02753 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L21-a (Q02753) · a predicted model of the same protein · chain BT against A, TM-score 0.91
P14120 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L30 (P14120) · a predicted model of the same protein · chain BZ against A, TM-score 0.91

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