Research workbench

Structure of the HCV ires bound to the human ribosome

Analyse Structure of the HCV ires bound to the human ribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5A2Q
Type: protein + RNA
Length: 6,867 residues
Chains: 38
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S rRNA; HCV ires; Ribosomal protein US2; Ribosomal protein ES1; Ribosomal protein US5…
UniProt: P08865, Q6NXR8, P15880, P23396, P62701, P46782, P62753, P62081, P62241, P46781, P46783, P62280, P25398, P62277, P62263, P62841, P62249, P08708, P62269, P39019, P60866, P63220, P62244, P62266, P62847, P62851, P62854, P42677, P62857, P62273, P62861, Q5RKT7, P63244, P62945, P84098, P83731
Ligands: MG, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 38 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S rRNA	rna	1665	—	—
3	HCV ires	rna	257	—	—
A	Ribosomal protein US2	protein	216	40% helix, 14% strand	P08865
B	Ribosomal protein ES1	protein	213	30% helix, 31% strand	Q6NXR8
C	Ribosomal protein US5	protein	218	34% helix, 29% strand	P15880
D	Ribosomal protein US3	protein	225	33% helix, 28% strand	P23396
E	Ribosomal protein ES4	protein	262	16% helix, 33% strand	P62701
F	Ribosomal protein US7	protein	189	50% helix, 7% strand	P46782
G	Ribosomal protein ES6	protein	230	28% helix, 27% strand	P62753
H	Ribosomal protein ES7	protein	186	37% helix, 23% strand	P62081
I	Ribosomal protein ES8	protein	205	32% helix, 27% strand	P62241
J	Ribosomal protein US4	protein	180	49% helix, 4% strand	P46781
K	Ribosomal protein ES10	protein	95	43% helix, 15% strand	P46783
L	Ribosomal protein US17	protein	151	5% helix, 32% strand	P62280
M	Ribosomal protein ES12	protein	123	41% helix, 14% strand	P25398
N	Ribosomal protein US15	protein	149	56% helix, 0% strand	P62277
O	Ribosomal protein US11	protein	135	27% helix, 25% strand	P62263
P	Ribosomal protein US19	protein	120	38% helix, 14% strand	P62841
Q	Ribosomal protein US9	protein	139	35% helix, 19% strand	P62249
R	Ribosomal protein ES17	protein	132	47% helix, 6% strand	P08708
S	Ribosomal protein US13	protein	143	39% helix, 8% strand	P62269
T	Ribosomal protein ES19	protein	145	51% helix, 10% strand	P39019
U	Ribosomal protein US10	protein	101	27% helix, 45% strand	P60866
V	Ribosomal protein ES21	protein	82	21% helix, 27% strand	P63220
W	Ribosomal protein US8	protein	129	32% helix, 26% strand	P62244
X	Ribosomal protein US12	protein	141	25% helix, 29% strand	P62266
Y	Ribosomal protein ES24	protein	124	34% helix, 29% strand	P62847
Z	Ribosomal protein ES25	protein	72	44% helix, 24% strand	P62851
a	Ribosomal protein ES26	protein	101	19% helix, 23% strand	P62854
b	Ribosomal protein ES27	protein	82	7% helix, 28% strand	P42677
c	Ribosomal protein ES28	protein	61	0% helix, 46% strand	P62857
d	Ribosomal protein US14	protein	55	20% helix, 9% strand	P62273
e	Ribosomal protein ES30	protein	56	23% helix, 0% strand	P62861
f	Ribosomal protein ES31	protein	72	4% helix, 19% strand	Q5RKT7
g	Ribosomal protein RACK1	protein	314	0% helix, 53% strand	P63244
h	Ribosomal protein EL41	protein	24	75% helix, 0% strand	P62945
r	Ribosomal protein EL19	protein	13	85% helix, 0% strand	P84098
w	Ribosomal protein EL24	protein	62	58% helix, 3% strand	P83731

Ligands and binding sites

MG · Magnesium ion · metal · 98 copies · chains 2, a, I, E, N, J, C, X
ZN · Zinc ion · metal · 3 copies · chains a, 2, d, f

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	1087	0.90	0.93	141	empty
2	921	0.88	0.90	114	empty
3	1014	0.88	0.90	94	empty
4	657	0.86	0.92	80	empty
5	813	0.86	0.90	83	MG

Interfaces

104 interfaces between chains.

2–G · 5322 Å² buried · 123 hydrogen bonds · protein-nucleic
2–I · 4270 Å² buried · 99 hydrogen bonds · protein-nucleic
2–E · 3957 Å² buried · 74 hydrogen bonds · protein-nucleic
2–J · 3671 Å² buried · 81 hydrogen bonds · protein-nucleic
2–X · 3507 Å² buried · 73 hydrogen bonds · protein-nucleic

Compared structures

5A2Q · Structure of the HCV IRES bound to the human ribosome · the same entry in another collection · chain H against H, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P08865
Every structure of UniProt Q6NXR8
Every structure of UniProt P15880
Every structure of UniProt P23396
Every structure of UniProt P62701
Every structure of UniProt P46782
Every structure of UniProt P62753
Every structure of UniProt P62081
Every structure of UniProt P62241
Every structure of UniProt P46781
Every structure of UniProt P46783
Every structure of UniProt P62280
Every structure of UniProt P25398
Every structure of UniProt P62277
Every structure of UniProt P62263
Every structure of UniProt P62841
Every structure of UniProt P62249
Every structure of UniProt P08708
Every structure of UniProt P62269
Every structure of UniProt P39019
Every structure of UniProt P60866
Every structure of UniProt P63220
Every structure of UniProt P62244
Every structure of UniProt P62266
Every structure of UniProt P62847
Every structure of UniProt P62851
Every structure of UniProt P62854
Every structure of UniProt P42677
Every structure of UniProt P62857
Every structure of UniProt P62273
Every structure of UniProt P62861
Every structure of UniProt Q5RKT7
Every structure of UniProt P63244
Every structure of UniProt P62945
Every structure of UniProt P84098
Every structure of UniProt P83731
Elsewhere: RCSB PDB 5A2Q · PDBe 5A2Q · UniProt P08865 · UniProt Q6NXR8 · UniProt P15880 · UniProt P23396 · UniProt P62701 · UniProt P46782 · UniProt P62753 · UniProt P62081 · UniProt P62241 · UniProt P46781 · UniProt P46783 · UniProt P62280 · UniProt P25398 · UniProt P62277 · UniProt P62263 · UniProt P62841 · UniProt P62249 · UniProt P08708 · UniProt P62269 · UniProt P39019 · UniProt P60866 · UniProt P63220 · UniProt P62244 · UniProt P62266 · UniProt P62847 · UniProt P62851 · UniProt P62854 · UniProt P42677 · UniProt P62857 · UniProt P62273 · UniProt P62861 · UniProt Q5RKT7 · UniProt P63244 · UniProt P62945 · UniProt P84098 · UniProt P83731

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