Het-PDB Navi2 (PDB: 4WRA)

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Data format:

Color scheme of protein:

Ligands
Code	Name	Link
MG	Magnesium ion	PoSSuM
PAR	Paromomycin	PoSSuM
ZN	Zinc ion	PoSSuM

Non-standard Residues
Code	Name	Show
QUO	2-amino-7-deaza-(2'',3''-dihydroxy-cyclopentylamino)-guanosine-5'-monophosphate
MIA	2-methylthio-n6-isopentenyl-adenosine-5'-monophosphate
PSU	Pseudouridine-5'-monophosphate
5MU	5-methyluridine 5'-monophosphate
4SU	4-thiouridine-5'-monophosphate
OMC	O2'-methylycytidine-5'-monophosphate

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show

Download interaction data: 4WRA

Code :

4WRA PDBj RCSB PDB PDBe

Header :

RIBOSOME

Title :

Complex of 70S ribosome with tRNA-Tyr and mRNA with A-A mismatch in the first position in the A-site and with antibiotic paromomycin.

Release Data :

2015-06-10

Compound :

mol_id	molecule	chains
1	16S ribosomal RNA	13,1G

mol_id	molecule	chains
2	30S ribosomal protein S2	1E,12

mol_id	molecule	chains
3	30S ribosomal protein S3	2E,22

mol_id	molecule	chains
4	30S ribosomal protein S4	3E,32

mol_id	molecule	chains
5	30S ribosomal protein S5	4E,42

mol_id	molecule	chains	synonym
6	30S ribosomal protein S6	5E,52	TS9

mol_id	molecule	chains
7	30S ribosomal protein S7	6E,62

mol_id	molecule	chains
8	30S ribosomal protein S8	7E,72

mol_id	molecule	chains
9	30S ribosomal protein S9	8E,82

mol_id	molecule	chains
10	30S ribosomal protein S10	1I,1A

mol_id	molecule	chains
11	30S ribosomal protein S11	2I,2A

mol_id	molecule	chains
12	30S ribosomal protein S12	3I,3A

mol_id	molecule	chains
13	30S ribosomal protein S13	4I,4A

mol_id	molecule	chains
14	30S ribosomal protein S14 type Z	5I,5A

mol_id	molecule	chains
15	30S ribosomal protein S15	6I,6A

mol_id	molecule	chains
16	30S ribosomal protein S16	7I,7A

mol_id	molecule	chains
17	30S ribosomal protein S17	8I,8A

mol_id	molecule	chains
18	30S ribosomal protein S18	9I,9A

mol_id	molecule	chains
19	30S ribosomal protein S19	AI,AA

mol_id	molecule	chains
20	30S ribosomal protein S20	BI,BA

mol_id	molecule	chains
21	30S ribosomal protein Thx	1F,1B

mol_id	molecule	chains
22	tRNA-Tyr	1K

mol_id	molecule	chains
23	tRNA-fMet	2K,2L

mol_id	molecule	chains
24	tRNA-Tyr	3K,1L

mol_id	molecule	chains
25	mRNA	4K,4L

mol_id	molecule	chains
26	23S ribosomal RNA	1H,14

mol_id	molecule	chains
27	5S ribosomal RNA	16,1J

mol_id	molecule	chains
28	50S ribosomal protein L2	11,19

mol_id	molecule	chains
29	50S ribosomal protein L3	21,29

mol_id	molecule	chains	synonym
30	50S ribosomal protein L4	31,39	L1e

mol_id	molecule	chains
31	50S ribosomal protein L5	41,49

mol_id	molecule	chains
32	50S ribosomal protein L6	51,59

mol_id	molecule	chains
33	50S ribosomal protein L9	61,69

mol_id	molecule	chains
34	50S ribosomal protein L13	58,15

mol_id	molecule	chains
35	50S ribosomal protein L14	68,25

mol_id	molecule	chains
36	50S ribosomal protein L15	78,35

mol_id	molecule	chains
37	50S ribosomal protein L16	88,45

mol_id	molecule	chains
38	50S ribosomal protein L17	98,55

mol_id	molecule	chains	synonym
39	50S ribosomal protein L18	A8,65	TL24

mol_id	molecule	chains
40	50S ribosomal protein L19	B8,75

mol_id	molecule	chains
41	50S ribosomal protein L20	C8,85

mol_id	molecule	chains
42	50S ribosomal protein L21	D8,95

mol_id	molecule	chains
43	50S ribosomal protein L22	E8,A5

mol_id	molecule	chains
44	50S ribosomal protein L23	F8,B5

mol_id	molecule	chains
45	50S ribosomal protein L24	G8,C5

mol_id	molecule	chains	synonym
46	50S ribosomal protein L25	H8,D5	TL5

mol_id	molecule	chains
47	50S ribosomal protein L27	I8,E5

mol_id	molecule	chains
48	50S ribosomal protein L28	J8,F5

mol_id	molecule	chains
49	50S ribosomal protein L29	K8,G5

mol_id	molecule	chains
50	50S ribosomal protein L30	L8,H5

mol_id	molecule	chains
51	50S ribosomal protein L31	M8,I5

mol_id	molecule	chains
52	50S ribosomal protein L32	N8,J5

mol_id	molecule	chains
53	50S ribosomal protein L34	P8,L5

mol_id	molecule	chains
54	50S ribosomal protein L35	Q8,M5

mol_id	molecule	chains
55	tRNA-Tyr	3L

Source :

mol_id	organism_scientific
1	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
2	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
3	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
4	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
5	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
6	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
7	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
8	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
9	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
10	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
11	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
12	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
13	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
14	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
15	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
16	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
17	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
18	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
19	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
20	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
21	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
22	Escherichia coli (taxid:562)

mol_id	organism_scientific
23	Escherichia coli (taxid:562)

mol_id	organism_scientific
24	Escherichia coli (taxid:562)

mol_id	organism_scientific
25	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
26	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
27	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
28	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
29	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
30	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
31	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
32	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
33	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
34	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
35	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
36	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
37	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
38	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
39	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
40	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
41	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
42	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
43	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
44	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
45	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
46	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
47	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
48	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
49	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
50	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
51	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
52	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
53	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
54	Thermus thermophilus HB8 (taxid:300852)

mol_id	organism_scientific
55	Escherichia coli (taxid:562)

Authors :

Rozov, A., Demeshkina, N., Yusupov, M., Yusupova, G.

Keywords :

ribosome, translation, mismatch

Exp. method :

X-RAY DIFFRACTION ( 3.05 Å )

Citation :

Structural insights into the translational infidelity mechanism.

Rozov, A.,Demeshkina, N.,Westhof, E. et al.
(2015) Nat Commun 6 : 7251 - 7251

PubMed: 26037619
DOI: 10.1038/ncomms8251

Chain :	1E, 12
UniProt :	P62662 (RS2_THET2)
Reaction :	-

Chain :	2E, 22
UniProt :	P62663 (RS3_THET2)
Reaction :	-

Chain :	3E, 32
UniProt :	P62664 (RS4_THET2)
Reaction :	-

Chain :	4E, 42
UniProt :	P27152 (RS5_THETH)
Reaction :	-

Chain :	5E, 52
UniProt :	P23370 (RS6_THETH)
Reaction :	-

Chain :	6E, 62
UniProt :	P62667 (RS7_THET2)
Reaction :	-

Chain :	7E, 72
UniProt :	P24319 (RS8_THETH)
Reaction :	-

Chain :	8E, 82
UniProt :	P80374 (RS9_THET8)
Reaction :	-

Chain :	1I, 1A
UniProt :	P80375 (RS10_THETH)
Reaction :	-

Chain :	2I, 2A
UniProt :	P62654 (RS11_THET2)
Reaction :	-

Chain :	3I, 3A
UniProt :	P17293 (RS12_THETH)
Reaction :	-

Chain :	4I, 4A
UniProt :	P62655 (RS13_THET2)
Reaction :	-

Chain :	5I, 5A
UniProt :	P24320 (RS14Z_THETH)
Reaction :	-

Chain :	6I, 6A
UniProt :	P80378 (RS15_THETH)
Reaction :	-

Chain :	7I, 7A
UniProt :	P62238 (RS16_THET2)
Reaction :	-

Chain :	8I, 8A
UniProt :	Q5SHP7 (RS17_THET8)
Reaction :	-

Chain :	9I, 9A
UniProt :	P62659 (RS18_THET2)
Reaction :	-

Chain :	AI, AA
UniProt :	P80381 (RS19_THETH)
Reaction :	-

Chain :	BI, BA
UniProt :	P80380 (RS20_THET8)
Reaction :	-

Chain :	1F, 1B
UniProt :	P62612 (RSHX_THETH)
Reaction :	-

Chain :	11, 19
UniProt :	P60405 (RL2_THET8)
Reaction :	-

Chain :	21, 29
UniProt :	Q5SHN8 (RL3_THET8)
Reaction :	-

Chain :	31, 39
UniProt :	Q5SHN9 (RL4_THET8)
Reaction :	-

Chain :	41, 49
UniProt :	Q5SHQ0 (RL5_THET8)
Reaction :	-

Chain :	51, 59
UniProt :	P24316 (RL6_THETH)
Reaction :	-

Chain :	61, 69
UniProt :	Q5SLQ1 (RL9_THET8)
Reaction :	-

Chain :	58, 15
UniProt :	P60488 (RL13_THET8)
Reaction :	-

Chain :	68, 25
UniProt :	Q5SHP8 (RL14_THET8)
Reaction :	-

Chain :	78, 35
UniProt :	Q5SHQ7 (RL15_THET8)
Reaction :	-

Chain :	88, 45
UniProt :	P60489 (RL16_THET8)
Reaction :	-

Chain :	98, 55
UniProt :	Q9Z9H5 (RL17_THET8)
Reaction :	-

Chain :	A8, 65
UniProt :	Q5SHQ4 (RL18_THET8)
Reaction :	-

Chain :	B8, 75
UniProt :	P60490 (RL19_THET8)
Reaction :	-

Chain :	C8, 85
UniProt :	P60491 (RL20_THET8)
Reaction :	-

Chain :	D8, 95
UniProt :	P60492 (RL21_THET8)
Reaction :	-

Chain :	E8, A5
UniProt :	Q5SHP3 (RL22_THET8)
Reaction :	-

Chain :	F8, B5
UniProt :	Q5SHP0 (RL23_THET8)
Reaction :	-

Chain :	G8, C5
UniProt :	Q5SHP9 (RL24_THET8)
Reaction :	-

Chain :	H8, D5
UniProt :	Q5SHZ1 (RL25_THET8)
Reaction :	-

Chain :	I8, E5
UniProt :	P60493 (RL27_THET8)
Reaction :	-

Chain :	J8, F5
UniProt :	P60494 (RL28_THET8)
Reaction :	-

Chain :	K8, G5
UniProt :	Q5SHP6 (RL29_THET8)
Reaction :	-

Chain :	L8, H5
UniProt :	Q5SHQ6 (RL30_THET8)
Reaction :	-

Chain :	M8, I5
UniProt :	Q5SJE1 (RL31_THET8)
Reaction :	-

Chain :	N8, J5
UniProt :	P80339 (RL32_THET8)
Reaction :	-

Chain :	P8, L5
UniProt :	P80340 (RL34_THET8)
Reaction :	-

Chain :	Q8, M5
UniProt :	Q5SKU1 (RL35_THET8)
Reaction :	-

PDB ID: 4WRA

Hetero Atom Contents

Structure summary

Reaction