Research workbench

Human collided disome (di-ribosome) stalled on XBP1 mRNA

Analyse Human collided disome (di-ribosome) stalled on XBP1 mRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QVP
Type: protein + RNA
Length: 33,648 residues
Chains: 162
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.0
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: mRNA; tRNA P/P; tRNA P/E; tNRA E/E; 5.8S ribosomal RNA; 28S ribosomal RNA; 5S ribosomal…
EC: 4.2.99.18
UniProt: A0A8B8VPA8, P39023, P36578, P46777, Q02878, P18124, P62424, P32969, Q96L21, P62913, P26373, P50914, L8Y0W1, P40429, P18621, Q07020, A0A2J8KH59, Q02543, P46778, P35268, A0A3P9HH38, F2X267, P62750, A0A5N3X333, A0A851LWS6, P46776, P47914, P62888, G7NZE1, P62910, P18077, A0A1U7T3M5, P42766, Q9Y3U8, A0A2Y9RW09, A0A1A7W9T9, A0A7N4PFJ2, A0A8C8Y9V5, P62945, J3KQN4, A0A6I9ZMF9, P46779, P08865, P61247, P15880, P23396, P62701, A0A6J0Y1Z7, P62753, P62082, P62241, A0A6J0B498, P46783, A0A8B8VW69, A0A663F1C0, A0A7L0BEC6, A0A2K6QL61, A0A4W2HV66, P08708, H0WTR0, A0A2Y9E7Q1, P60868, P63220, A0A2K5QKS6, A0A340WVW7, P62847, A0A6J3IG71, A0A6J2NCX2, A0A7J8BG50, A0A3M0JHZ8, A0A2J8WKD7, A0A2K6U587, A0A671DUR2, A0A2K6K8B0, A0A8C0T835
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.0 · 132 distinct chains · 31% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A4	mRNA	rna	14	—	—
A5	mRNA	rna	11	—	—
B4	tRNA P/P	rna	76	—	—
B5	tRNA P/E	rna	75	—	—
CC	tNRA E/E	rna	75	—	—
D5	tRNA P/P	rna	73	—	—
L1, L8	5.8S ribosomal RNA	rna	156	—	—
L5	28S ribosomal RNA	rna	3611	—	—
L6	28S ribosomal RNA	rna	3572	—	—
L7, L9	5S ribosomal RNA	rna	120	—	—
LA, MA	60S ribosomal protein L8	protein	248	8% helix, 27% strand	A0A8B8VPA8
LB	60S ribosomal protein L3	protein	395	15% helix, 28% strand	P39023
LC	60S ribosomal protein L4	protein	364	35% helix, 10% strand	P36578
LD, MD	60S ribosomal protein L5	protein	293	42% helix, 11% strand	P46777
LE	60S ribosomal protein L6	protein	219	21% helix, 15% strand	Q02878
LF, MF	60S ribosomal protein L7	protein	225	54% helix, 13% strand	P18124
LG	60S ribosomal protein L7a	protein	229	49% helix, 9% strand	P62424
LH	60S ribosomal protein L9	protein	190	19% helix, 39% strand	P32969
LI	60S ribosomal protein L10-like	protein	206	24% helix, 25% strand	Q96L21
LJ	60S ribosomal protein L11	protein	169	30% helix, 24% strand	P62913
LL	60S ribosomal protein L13	protein	205	42% helix, 10% strand	P26373
LM	60S ribosomal protein L14	protein	139	45% helix, 25% strand	P50914
LN, MN	60S ribosomal protein L15	protein	203	39% helix, 17% strand	L8Y0W1
LO	60S ribosomal protein L13a	protein	200	56% helix, 11% strand	P40429
LP, MP	60S ribosomal protein L17	protein	153	31% helix, 27% strand	P18621
LQ, MQ	60S ribosomal protein L18	protein	187	30% helix, 14% strand	Q07020
LR	60S ribosomal protein L19	protein	176	67% helix, 3% strand	A0A2J8KH59
LS, MS	60S ribosomal protein L18a	protein	175	22% helix, 31% strand	Q02543
LT, MT	60S ribosomal protein L21	protein	159	19% helix, 23% strand	P46778
LU, MU	60S ribosomal protein L22	protein	101	34% helix, 31% strand	P35268
LV, MV	60S ribosomal protein L23	protein	131	14% helix, 33% strand	A0A3P9HH38
LW	60S ribosomal protein L24	protein	115	36% helix, 10% strand	F2X267
LX, MX	60S ribosomal protein L23a	protein	120	28% helix, 23% strand	P62750
LY, MY	KOW domain-containing protein	protein	134	31% helix, 25% strand	A0A5N3X333
LZ, MZ	60S ribosomal protein L27	protein	135	24% helix, 28% strand	A0A851LWS6
La	60S ribosomal protein L27a	protein	147	25% helix, 14% strand	P46776
Lb	60S ribosomal protein L29	protein	75	55% helix, 0% strand	P47914
Lc	60S ribosomal protein L30	protein	97	44% helix, 19% strand	P62888
Ld, Md	60S ribosomal protein L31	protein	107	29% helix, 22% strand	G7NZE1
Le	60S ribosomal protein L32	protein	128	18% helix, 9% strand	P62910
Lf, Mf	60S ribosomal protein L35a	protein	109	3% helix, 50% strand	P18077
Lg	60S ribosomal protein L34	protein	114	30% helix, 9% strand	A0A1U7T3M5
Lh, Mh	60S ribosomal protein L35	protein	121	65% helix, 2% strand	P42766
Li	60S ribosomal protein L36	protein	102	63% helix, 1% strand	Q9Y3U8
Lj, Mj	Ribosomal protein L37	protein	86	26% helix, 7% strand	A0A2Y9RW09
Lk, Mk	60S ribosomal protein L38	protein	69	25% helix, 35% strand	A0A1A7W9T9
Ll, Ml	60S ribosomal protein L39	protein	50	32% helix, 0% strand	A0A7N4PFJ2
Lm	Ubiquitin-60S ribosomal protein L40	protein	52	21% helix, 15% strand	A0A8C8Y9V5
Ln, Mn	60S ribosomal protein L41	protein	24	83% helix, 0% strand	P62945
Lo	60S ribosomal protein L36a	protein	105	10% helix, 30% strand	J3KQN4
Lp, Mp	60S ribosomal protein L37a	protein	91	42% helix, 15% strand	A0A6I9ZMF9
Lr, Mr	60S ribosomal protein L28	protein	125	34% helix, 18% strand	P46779
MB	60S ribosomal protein L3	protein	393	16% helix, 26% strand	P39023
MC	60S ribosomal protein L4	protein	365	35% helix, 10% strand	P36578
ME	60S ribosomal protein L6	protein	220	19% helix, 19% strand	Q02878
MG	60S ribosomal protein L7a	protein	229	50% helix, 9% strand	P62424
MH	60S ribosomal protein L9	protein	189	22% helix, 35% strand	P32969
MI	60S ribosomal protein L10-like	protein	203	23% helix, 25% strand	Q96L21
MJ	60S ribosomal protein L11	protein	167	27% helix, 22% strand	P62913
ML	60S ribosomal protein L13	protein	204	38% helix, 7% strand	P26373
MM	60S ribosomal protein L14	protein	136	42% helix, 26% strand	P50914
MO	60S ribosomal protein L13a	protein	201	52% helix, 10% strand	P40429
MR	60S ribosomal protein L19	protein	175	62% helix, 3% strand	A0A2J8KH59
MW	60S ribosomal protein L24	protein	115	34% helix, 10% strand	F2X267
Ma	60S ribosomal protein L27a	protein	146	28% helix, 13% strand	P46776
Mb	60S ribosomal protein L29	protein	63	44% helix, 0% strand	P47914
Mc	60S ribosomal protein L30	protein	93	40% helix, 19% strand	P62888
Me	60S ribosomal protein L32	protein	127	16% helix, 9% strand	P62910
Mg	60S ribosomal protein L34	protein	110	31% helix, 9% strand	A0A1U7T3M5
Mi	60S ribosomal protein L36	protein	101	62% helix, 0% strand	Q9Y3U8
Mm	Ubiquitin-60S ribosomal protein L40	protein	50	22% helix, 16% strand	A0A8C8Y9V5
Mo	60S ribosomal protein L36a	protein	98	9% helix, 31% strand	J3KQN4
RA	40S ribosomal protein SA	protein	212	38% helix, 11% strand	P08865
RB	40S ribosomal protein S3a	protein	214	30% helix, 29% strand	P61247
RC	40S ribosomal protein S2	protein	217	34% helix, 28% strand	P15880
RD	40S ribosomal protein S3 (EC 4.2.99.18)	protein	215	38% helix, 21% strand	P23396
RE	40S ribosomal protein S4, X isoform	protein	257	16% helix, 25% strand	P62701
RF	40S ribosomal protein S5	protein	180	51% helix, 5% strand	A0A6J0Y1Z7
RG	40S ribosomal protein S6	protein	213	23% helix, 18% strand	P62753
RH	40S ribosomal protein S7	protein	176	36% helix, 18% strand	P62082
RI	40S ribosomal protein S8	protein	187	26% helix, 29% strand	P62241
RJ	40S ribosomal protein S9	protein	176	45% helix, 4% strand	A0A6J0B498
RK	40S ribosomal protein S10	protein	95	36% helix, 13% strand	P46783
RL	40S ribosomal protein S11	protein	140	3% helix, 34% strand	A0A8B8VW69
RN, SN	40S ribosomal protein S13	protein	150	51% helix, 0% strand	A0A663F1C0
RO	40S ribosomal protein S14	protein	135	27% helix, 18% strand	A0A7L0BEC6
RP	40S ribosomal protein S15	protein	127	31% helix, 13% strand	A0A2K6QL61
RQ	40S ribosomal protein S16	protein	141	36% helix, 17% strand	A0A4W2HV66
RR	40S ribosomal protein S17	protein	125	51% helix, 1% strand	P08708
RS	40S ribosomal protein S18	protein	138	38% helix, 6% strand	H0WTR0
RT	40S ribosomal protein S19	protein	141	49% helix, 14% strand	A0A2Y9E7Q1
RU	40S ribosomal protein S20	protein	100	21% helix, 37% strand	P60868
RV, SV	40S ribosomal protein S21	protein	83	17% helix, 24% strand	P63220
RW, SW	40S ribosomal protein S15a	protein	129	30% helix, 21% strand	A0A2K5QKS6
RX, SX	40S ribosomal protein S23	protein	141	20% helix, 18% strand	A0A340WVW7
RY	40S ribosomal protein S24	protein	113	30% helix, 32% strand	P62847
RZ	40S ribosomal protein S25	protein	70	44% helix, 9% strand	A0A6J3IG71
Ra, Sa	40S ribosomal protein S26	protein	99	13% helix, 18% strand	A0A6J2NCX2
Rb, Sb	40S ribosomal protein S27	protein	83	5% helix, 23% strand	A0A7J8BG50
Rc	40S ribosomal protein S28	protein	61	5% helix, 39% strand	A0A3M0JHZ8
Rd	40S ribosomal protein S29	protein	52	19% helix, 10% strand	A0A2J8WKD7
Re	40S ribosomal protein S30	protein	51	33% helix, 0% strand	A0A2K6U587
Rf	40S ribosomal protein S12	protein	78	33% helix, 10% strand	A0A671DUR2
Rg	Receptor of activated protein C kinase 1	protein	283	0% helix, 34% strand	A0A2K6K8B0
Rh	Ubiquitin-40S ribosomal protein S27a	protein	41	0% helix, 5% strand	A0A8C0T835
S2	18S ribosomal RNA	rna	1714	—	—
S3	18S ribosomal RNA	rna	1705	—	—
SA	40S ribosomal protein SA	protein	216	41% helix, 13% strand	P08865
SB	40S ribosomal protein S3a	protein	213	30% helix, 31% strand	P61247
SC	40S ribosomal protein S2	protein	219	30% helix, 26% strand	P15880
SD	40S ribosomal protein S3 (EC 4.2.99.18)	protein	223	34% helix, 22% strand	P23396
SE	40S ribosomal protein S4, X isoform	protein	262	16% helix, 27% strand	P62701
SF	40S ribosomal protein S5	protein	187	50% helix, 4% strand	A0A6J0Y1Z7
SG	40S ribosomal protein S6	protein	231	27% helix, 19% strand	P62753
SH	40S ribosomal protein S7	protein	183	34% helix, 22% strand	P62082
SI	40S ribosomal protein S8	protein	206	26% helix, 25% strand	P62241
SJ	40S ribosomal protein S9	protein	179	48% helix, 5% strand	A0A6J0B498
SK	40S ribosomal protein S10	protein	96	40% helix, 15% strand	P46783
SL	40S ribosomal protein S11	protein	144	3% helix, 29% strand	A0A8B8VW69
SO	40S ribosomal protein S14	protein	134	23% helix, 22% strand	A0A7L0BEC6
SP	40S ribosomal protein S15	protein	128	35% helix, 15% strand	A0A2K6QL61
SQ	40S ribosomal protein S16	protein	142	35% helix, 14% strand	A0A4W2HV66
SR	40S ribosomal protein S17	protein	131	47% helix, 6% strand	P08708
SS	40S ribosomal protein S18	protein	141	35% helix, 3% strand	H0WTR0
ST	40S ribosomal protein S19	protein	143	51% helix, 9% strand	A0A2Y9E7Q1
SU	40S ribosomal protein S20	protein	101	22% helix, 37% strand	P60868
SY	40S ribosomal protein S24	protein	123	31% helix, 31% strand	P62847
SZ	40S ribosomal protein S25	protein	75	41% helix, 12% strand	A0A6J3IG71
Sc	40S ribosomal protein S28	protein	63	0% helix, 30% strand	A0A3M0JHZ8
Sd	40S ribosomal protein S29	protein	53	26% helix, 11% strand	A0A2J8WKD7
Se	40S ribosomal protein S30	protein	57	30% helix, 0% strand	A0A2K6U587
Sg	Receptor of activated protein C kinase 1	protein	308	0% helix, 41% strand	A0A2K6K8B0

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	1014	0.90	0.93	84	empty
2	1107	0.89	0.92	94	empty
3	1025	0.89	0.92	97	empty
4	1062	0.89	0.91	88	empty
5	1432	0.89	0.91	117	empty

Interfaces

523 interfaces between chains.

L6–MB · 9257 Å² buried · 214 hydrogen bonds · protein-nucleic
L5–LB · 9152 Å² buried · 216 hydrogen bonds · protein-nucleic
L6–MC · 9137 Å² buried · 196 hydrogen bonds · protein-nucleic
L5–LC · 9094 Å² buried · 190 hydrogen bonds · protein-nucleic
L6–MA · 7542 Å² buried · 171 hydrogen bonds · protein-nucleic

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 LB 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 LO 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 LP against A, TM-score 0.99
Q96L21 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L10-like (Q96L21) · a predicted model of the same protein · chain LI against A, TM-score 0.99
P15880 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S2 (P15880) · a predicted model of the same protein · chain SC against A, TM-score 0.99
Q02543 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L18A (Q02543) · a predicted model of the same protein · chain LS against A, TM-score 0.99
P46779 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L28 (P46779) · a predicted model of the same protein · chain Lr against A, TM-score 0.99
P32969 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L9 (P32969) · a predicted model of the same protein · chain LH against A, TM-score 0.98

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