Brand  (β version)

PDB ID: 6AZ1

Hetero Atom Contents

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Ligands
Code Name Style Show Link
MG Magnesium ion PoSSuM
PAR Paromomycin PoSSuM
Non-standard Residues
Code Name Show
4OC 4n,o2'-methylcytidine-5'-monophosphate
5MC 5-methylcytidine-5'-monophosphate
7MG 7n-methyl-8-hydroguanosine-5'-monophosphate
A2M 2'-O-methyladenosine 5'-(dihydrogen phosphate)
C4J (5s)-5-{3-[(3s)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol
M1Y (1s)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-xylitol
MA6 6n-dimethyladenosine-5'-monophoshate
MIA 2-methylthio-n6-isopentenyl-adenosine-5'-monophosphate
OMC O2'-methylycytidine-5'-monophosphate
OMG O2'-methylguanosine-5'-monophosphate
OMU O2'-methyluridine 5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 6AZ1   PDBj   RCSB PDB   PDBe
Header : RIBOSOME/ANTIBIOTIC
Title : Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin
Release Data : 2017-12-06
Compound :
mol_id molecule chains
1 Ribosomal protein s1e A
mol_id molecule chains
2 ribosomal protein S2 B
mol_id molecule chains
3 ribosomal protein S3 C
mol_id molecule chains
4 ribosomal protein S4 D
mol_id molecule chains
5 ribosomal protein S4e E
mol_id molecule chains
6 ribosomal protein S5 F
mol_id molecule chains
7 ribosomal protein S6e G
mol_id molecule chains
8 ribosomal protein S7 H
mol_id molecule chains
9 ribosomal protein S7e I
mol_id molecule chains
10 ribosomal protein S8 J
mol_id molecule chains
11 ribosomal protein S8e K
mol_id molecule chains
12 ribosomal protein S9 L
mol_id molecule chains
13 ribosomal protein S10 M
mol_id molecule chains
14 ribosomal protein S10e N
mol_id molecule chains
15 ribosomal protein S11 O
mol_id molecule chains
16 ribosomal protein S12 P
mol_id molecule chains
17 ribosomal protein S12e Q
mol_id molecule chains
18 ribosomal protein S13 R
mol_id molecule chains
19 ribosomal protein S14 S
mol_id molecule chains
20 ribosomal protein S15 T
mol_id molecule chains
21 ribosomal protein S17 U
mol_id molecule chains
22 ribosomal protein S17e V
mol_id molecule chains
23 ribosomal protein S19 W
mol_id molecule chains
24 ribosomal protein S19e X
mol_id molecule chains
25 ribosomal protein S21e Y
mol_id molecule chains
26 ribosomal protein S24e Z
mol_id molecule chains
27 ribosomal protein S25e a
mol_id molecule chains
28 ribosomal protein S26e b
mol_id molecule chains
29 ribosomal protein S27e c
mol_id molecule chains
30 ribosomal protein S28e d
mol_id molecule chains
31 ribosomal protein S30e e
mol_id molecule chains
32 ribosomal protein S31e f
mol_id molecule chains
33 LACK1 g
mol_id molecule chains
34 ribosomal RNA 18S 1
mol_id molecule chains
35 tRNA-Phe 2
mol_id molecule chains
36 P-site tRNA 3
mol_id molecule chains
37 E-site tRNA 4
mol_id molecule chains
38 mRNA 5
Source :
mol_id organism_scientific
1 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
2 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
3 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
4 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
5 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
6 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
7 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
8 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
9 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
10 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
11 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
12 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
13 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
14 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
15 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
16 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
17 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
18 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
19 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
20 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
21 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
22 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
23 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
24 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
25 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
26 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
27 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
28 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
29 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
30 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
31 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
32 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
33 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
34 Leishmania donovani  (taxid:5661)
mol_id organism_scientific
35 Escherichia coli  (taxid:562)
synthetic: yes
mol_id organism_scientific
36 Escherichia coli  (taxid:562)
mol_id organism_scientific
37 Escherichia coli  (taxid:562)
mol_id organism_scientific
38 Leishmania donovani  (taxid:5661)
synthetic: yes
Authors : Shalev-Benami, M., Zhang, Y., Rozenberg, H., Matzov, D., Zimmerman, E., Bashan, A., Jaffe, C.L., Yonath, A., Skiniotis, G.
Keywords : Leishmania donovani, ribosome, aminoglycoside, paromomycin, RIBOSOME-ANTIBIOTIC complex
Exp. method : ELECTRON MICROSCOPY ( 2.7 Å )
Citation :

Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.

Shalev-Benami, M.,Zhang, Y.,Rozenberg, H.  et al.
(2017)  Nat Commun  8 : 1589 - 1589

PubMed: 29150609
DOI: 10.1038/s41467-017-01664-4

Reaction

Chain : A
UniProt : E9BRS2 (E9BRS2_LEIDO)
Reaction : -
Chain : C
UniProt : E9BQ25 (E9BQ25_LEIDO)
Reaction : -
Chain : D
UniProt : E9BTJ0
Reaction : -
Chain : E
UniProt : E9BBI6
Reaction : -
Chain : F
UniProt : E9BNF0
Reaction : -
Chain : I
UniProt : E9B7A8
Reaction : -
Chain : J
UniProt : E9BAV6 (E9BAV6_LEIDO)
Reaction : -
Chain : K
UniProt : E9BH78
Reaction : -
Chain : L
UniProt : E9BI96 (E9BI96_LEIDO)
Reaction : -
Chain : N
UniProt : E9BTG4 (E9BTG4_LEIDO)
Reaction : -
Chain : O
UniProt : E9BMA8
Reaction : -
Chain : P
UniProt : E9BFB6 (E9BFB6_LEIDO)
Reaction : -
Chain : Q
UniProt : E9BBC0
Reaction : -
Chain : R
UniProt : E9BTF9 (E9BTF9_LEIDO)
Reaction : -
Chain : S
UniProt : E9BJV7 (E9BJV7_LEIDO)
Reaction : -
Chain : T
UniProt : E9BPR7
Reaction : -
Chain : V
UniProt : E9BJZ5 (E9BJZ5_LEIDO)
Reaction : -
Chain : X
UniProt : E9BR60 (E9BR60_LEIDO)
Reaction : -
Chain : Z
UniProt : E9BU11
Reaction : -
Chain : a
UniProt : E9BHM6 (E9BHM6_LEIDO)
Reaction : -
Chain : b
UniProt : E9BK95 (E9BK95_LEIDO)
Reaction : -
Chain : c
UniProt : E9BUA2
Reaction : -
Chain : d
UniProt : E9BIH3 (E9BIH3_LEIDO)
Reaction : -
Chain : e
UniProt : E9BLG3 (E9BLG3_LEIDO)
Reaction : -
Chain : f
UniProt : E9BTC5
Reaction : -
Chain : g
UniProt : Q9BIJ5 (Q9BIJ5_LEIDO)
Reaction : -