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Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC)

Analyse Structure of human ribosome nascent chain complex selectively stalled by a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OLI
Type: protein + RNA
Length: 17,147 residues
Chains: 83
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.5
Source: Homo sapiens
Molecule: 18S ribosomal RNA; 40S ribosomal protein SA; 40S ribosomal protein S3a; 40S ribosomal…
UniProt: P08865, P61247, P23396, P62701, P46782, P62081, P62241, P46783, P62280, P62841, P62249, P08708, P62269, P39019, P60866, P63220, P62266, P62854, P62857, P62273, P63244, P15880, P62753, P46781, P25398, P62277, P62263, P62244, P62847, P62851, P42677, E9PR30, P62979, P62917, P39023, P36578, P46777, Q02878, P18124, P62424, P32969, P27635, P62913, P26373, P50914, P61313, P40429, P18621, Q07020, P84098, Q02543, P46778, P35268, Q9BTQ7, P83731, P62750, P61254, P61353, P46776, P47914, P62888, P62899, P62910, P18077, P49207, P42766, Q9Y3U8, P61927, P63173, P62891, P62987, P62945, P83881, P61513, P46779
Ligands: MVM, MG, ZN
Pockets: 20 · best druggability 0.91

Structure

electron microscopy · resolution 3.5 · 83 distinct chains · 26% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
S2	18S ribosomal RNA	rna	1714	—	—
SA	40S ribosomal protein SA	protein	221	35% helix, 13% strand	P08865
SB	40S ribosomal protein S3a	protein	214	22% helix, 28% strand	P61247
SD	40S ribosomal protein S3	protein	226	29% helix, 19% strand	P23396
SE	40S ribosomal protein S4, X isoform	protein	259	9% helix, 28% strand	P62701
SF	40S ribosomal protein S5	protein	189	47% helix, 4% strand	P46782
SH	40S ribosomal protein S7	protein	186	29% helix, 19% strand	P62081
SI	40S ribosomal protein S8	protein	204	20% helix, 24% strand	P62241
SK	40S ribosomal protein S10	protein	98	36% helix, 8% strand	P46783
SL	40S ribosomal protein S11	protein	153	2% helix, 30% strand	P62280
SP	40S ribosomal protein S15	protein	127	24% helix, 12% strand	P62841
SQ	40S ribosomal protein S16	protein	146	27% helix, 18% strand	P62249
SR	40S ribosomal protein S17	protein	134	44% helix, 1% strand	P08708
SS	40S ribosomal protein S18	protein	145	38% helix, 6% strand	P62269
ST	40S ribosomal protein S19	protein	143	47% helix, 8% strand	P39019
SU	40S ribosomal protein S20	protein	104	20% helix, 29% strand	P60866
SV	40S ribosomal protein S21	protein	82	18% helix, 17% strand	P63220
SX	40S ribosomal protein S23	protein	141	18% helix, 24% strand	P62266
Sa	40S ribosomal protein S26	protein	102	9% helix, 20% strand	P62854
Sc	40S ribosomal protein S28	protein	64	0% helix, 27% strand	P62857
Sd	40S ribosomal protein S29	protein	55	25% helix, 5% strand	P62273
Sg	Receptor of activated protein C kinase 1	protein	312	0% helix, 44% strand	P63244
SC	40S ribosomal protein S2	protein	220	28% helix, 25% strand	P15880
SG	40S ribosomal protein S6	protein	237	17% helix, 23% strand	P62753
SJ	40S ribosomal protein S9	protein	185	33% helix, 5% strand	P46781
SM	40S ribosomal protein S12	protein	118	22% helix, 6% strand	P25398
SN	40S ribosomal protein S13	protein	150	49% helix, 0% strand	P62277
SO	40S ribosomal protein S14	protein	137	24% helix, 17% strand	P62263
SW	40S ribosomal protein S15a	protein	129	28% helix, 28% strand	P62244
SY	40S ribosomal protein S24	protein	131	20% helix, 29% strand	P62847
SZ	40S ribosomal protein S25	protein	73	38% helix, 10% strand	P62851
Sb	40S ribosomal protein S27	protein	82	6% helix, 22% strand	P42677
Se	40S ribosomal protein S30	protein	57	30% helix, 0% strand	E9PR30
Sf	40S ribosomal protein S27a	protein	67	0% helix, 9% strand	P62979
A	60S ribosomal protein L8	protein	252	10% helix, 26% strand	P62917
B	60S ribosomal protein L3	protein	397	13% helix, 25% strand	P39023
C	60S ribosomal protein L4	protein	363	36% helix, 10% strand	P36578
D	5.8S ribosomal RNA	rna	157	—	—
E	5S ribosomal RNA	rna	119	—	—
F	60S ribosomal protein L5	protein	294	36% helix, 11% strand	P46777
G	60S ribosomal protein L6	protein	236	15% helix, 14% strand	Q02878
H	60S ribosomal protein L7	protein	225	49% helix, 12% strand	P18124
I	60S ribosomal protein L7a	protein	234	41% helix, 8% strand	P62424
J	60S ribosomal protein L9	protein	191	18% helix, 38% strand	P32969
K	60S ribosomal protein L10	protein	208	21% helix, 25% strand	P27635
L	60S ribosomal protein L11	protein	169	30% helix, 18% strand	P62913
M	60S ribosomal protein L13	protein	205	33% helix, 7% strand	P26373
N	60S ribosomal protein L14	protein	139	47% helix, 27% strand	P50914
O	60S ribosomal protein L15	protein	203	28% helix, 16% strand	P61313
P	60S ribosomal protein L13a	protein	195	46% helix, 11% strand	P40429
Q	60S ribosomal protein L17	protein	153	27% helix, 32% strand	P18621
R	60S ribosomal protein L18	protein	187	22% helix, 10% strand	Q07020
S	60S ribosomal protein L19	protein	181	56% helix, 0% strand	P84098
T	60S ribosomal protein L18a	protein	175	18% helix, 27% strand	Q02543
U	60S ribosomal protein L21	protein	157	17% helix, 22% strand	P46778
V	60S ribosomal protein L22	protein	99	27% helix, 28% strand	P35268
W	60S ribosomal protein L23	protein	129	8% helix, 34% strand	Q9BTQ7
X	60S ribosomal protein L24	protein	61	23% helix, 16% strand	P83731
Y	60S ribosomal protein L23a	protein	117	17% helix, 24% strand	P62750
Z	60S ribosomal protein L26	protein	134	29% helix, 24% strand	P61254
a	60S ribosomal protein L27	protein	134	17% helix, 27% strand	P61353
b	60S ribosomal protein L27a	protein	147	20% helix, 15% strand	P46776
c	60S ribosomal protein L29	protein	100	38% helix, 0% strand	P47914
d	60S ribosomal protein L30	protein	103	39% helix, 17% strand	P62888
e	60S ribosomal protein L31	protein	106	26% helix, 28% strand	P62899
f	60S ribosomal protein L32	protein	129	20% helix, 7% strand	P62910
g	60S ribosomal protein L35a	protein	109	3% helix, 51% strand	P18077
h	60S ribosomal protein L34	protein	114	23% helix, 9% strand	P49207
i	60S ribosomal protein L35	protein	122	58% helix, 2% strand	P42766
j	60S ribosomal protein L36	protein	97	53% helix, 3% strand	Q9Y3U8
k	60S ribosomal protein L37	protein	84	18% helix, 6% strand	P61927
l	60S ribosomal protein L38	protein	69	20% helix, 32% strand	P63173
m	60S ribosomal protein L39	protein	50	24% helix, 0% strand	P62891
n	60S ribosomal protein L40	protein	50	22% helix, 14% strand	P62987
o	60S ribosomal protein L41	protein	25	64% helix, 0% strand	P62945
p	60S ribosomal protein L36a	protein	105	9% helix, 29% strand	P83881
q	60S ribosomal protein L37a	protein	91	36% helix, 14% strand	P61513
r	60S ribosomal protein L28	protein	122	20% helix, 17% strand	P46779
t	28S ribosomal RNA	rna	3607	—	—
u	tRNA	rna	76	—	—
v	tRNA	rna	76	—	—
w	mRNA	rna	10	—	—
y	Nascent chain	protein	36	0% helix, 0% strand	—

Ligands and binding sites

MVM · N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide · ligand · chains Q, t, y
MG · Magnesium ion · metal · 31 copies · chains S2, SF, B, t, D, E, H, F, O, b, o, A, Z, f
ZN · Zinc ion · metal · 6 copies · chains S2, Sa, Sf, k, p, q

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	977	0.91	0.94	125	empty
2	1189	0.89	0.91	118	empty
3	1182	0.89	0.91	103	MG
4	1169	0.88	0.91	121	empty
5	978	0.88	0.91	88	empty

Interfaces

269 interfaces between chains.

B–t · 9270 Å² buried · 184 hydrogen bonds · protein-nucleic
C–t · 8881 Å² buried · 172 hydrogen bonds · protein-nucleic
A–t · 7629 Å² buried · 161 hydrogen bonds · protein-nucleic
O–t · 7310 Å² buried · 149 hydrogen bonds · protein-nucleic
G–t · 6354 Å² buried · 136 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 34 modified, 6 disulfide, 2 isopeptide (nucleotide modification, disulfide, isopeptide).

Compared structures

P62701 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S4, X isoform (P62701) · a predicted model of the same protein · chain SE against A, TM-score 0.99
P39023 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3 (P39023) · a predicted model of the same protein · chain B against A, TM-score 0.99
P61313 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L15 (P61313) · a predicted model of the same protein · chain O against A, TM-score 0.99
P18621 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L17 (P18621) · a predicted model of the same protein · chain Q against A, TM-score 0.99
P62917 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L8 (P62917) · a predicted model of the same protein · chain A against A, TM-score 0.99
P40429 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L13A (P40429) · a predicted model of the same protein · chain P against A, TM-score 0.98
P62913 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L11 (P62913) · a predicted model of the same protein · chain L against A, TM-score 0.98
Q07020 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L18 (Q07020) · a predicted model of the same protein · chain R against A, TM-score 0.98
P62244 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S15A (P62244) · a predicted model of the same protein · chain SW against A, TM-score 0.98
P36578 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L4 (P36578) · a predicted model of the same protein · chain C against A, TM-score 0.98
P62277 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S13 (P62277) · a predicted model of the same protein · chain SN against A, TM-score 0.98
P61254 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26 (P61254) · a predicted model of the same protein · chain Z against A, TM-score 0.98

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