3I56 image
Deposition Date 2009-07-03
Release Date 2010-03-09
Last Version Date 2024-02-21
Entry Detail
PDB ID:
3I56
Keywords:
RIBOSOME/ANTIBIOTIC
Title:
Co-crystal structure of Triacetyloleandomcyin Bound to the Large Ribosomal Subunit
Biological Source:
Source Organism:
Haloarcula marismortui (Taxon ID: 2238)
Haloarcula marismortui ATCC 43049 (Taxon ID: 272569)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.90 Å
R-Value Free:
0.24
R-Value Work:
0.19
Space Group:
C 2 2 21
3I56 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:DA (auth: 0)
Chain Length:2923
Number of Molecules:1
Biological Source:Haloarcula marismortui ATCC 43049
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37e
Gene (Uniprot):rpl37e
Chain IDs:AA (auth: 1)
Chain Length:57
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P32410 Pfam ID:PF01907
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L39e
Gene (Uniprot):rpl39e
Chain IDs:BA (auth: 2)
Chain Length:50
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P22452 Pfam ID:PF00832
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L44E
Gene (Uniprot):rpl44e
Chain IDs:CA (auth: 3)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P32411 Pfam ID:PF00935
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:EA (auth: 9)
Chain Length:122
Number of Molecules:1
Biological Source:Haloarcula marismortui
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2P
Gene (Uniprot):rpl2
Chain IDs:A
Chain Length:240
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P20276 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3P
Gene (Uniprot):rpl3
Chain IDs:B
Chain Length:338
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P20279 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4P
Gene (Uniprot):rpl4
Chain IDs:C
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12735 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5P
Gene (Uniprot):rpl5
Chain IDs:D
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14124 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6P
Gene (Uniprot):rpl6
Chain IDs:E
Chain Length:178
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14135 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7Ae
Gene (Uniprot):rpl7ae
Chain IDs:F
Chain Length:120
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12743 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10E
Gene (Uniprot):rpl10
Chain IDs:G
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P15825 Pfam ID:PF00466, PF17777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10e
Gene (Uniprot):rpl10e
Chain IDs:H
Chain Length:174
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60617 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11P
Gene (Uniprot):rpl11
Chain IDs:I
Chain Length:162
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14122 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13P
Gene (Uniprot):rpl13
Chain IDs:J
Chain Length:145
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P29198 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14P
Gene (Uniprot):rpl14
Chain IDs:K
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P22450 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15P
Gene (Uniprot):rpl15
Chain IDs:L
Chain Length:165
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12737 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15e
Gene (Uniprot):rpl15e
Chain IDs:M
Chain Length:194
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60618 Pfam ID:PF00827
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18P
Gene (Uniprot):rpl18
Chain IDs:N
Chain Length:187
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14123 Pfam ID:PF17144
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18e
Gene (Uniprot):rpl18e
Chain IDs:O
Chain Length:116
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12733 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19e
Gene (Uniprot):rpl19e
Chain IDs:P
Chain Length:149
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14119 Pfam ID:PF01280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21e
Gene (Uniprot):rpl21e
Chain IDs:Q
Chain Length:96
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12734 Pfam ID:PF01157
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22P
Gene (Uniprot):rpl22
Chain IDs:R
Chain Length:155
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10970 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23P
Gene (Uniprot):rpl23
Chain IDs:S
Chain Length:85
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12732 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24P
Gene (Uniprot):rpl24
Chain IDs:T
Chain Length:120
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10972 Pfam ID:PF00467, PF16906
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24e
Gene (Uniprot):rpl24e
Chain IDs:U
Chain Length:66
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14116 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29P
Gene (Uniprot):rpl29
Chain IDs:V
Chain Length:71
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10971 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30P
Gene (Uniprot):rpl30
Chain IDs:W
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14121 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31e
Gene (Uniprot):rpl31e
Chain IDs:X
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P18138 Pfam ID:PF01198
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32e
Gene (Uniprot):rpl32e
Chain IDs:Y
Chain Length:241
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12736 Pfam ID:PF01655, PF14520
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37Ae
Gene (Uniprot):rpl37ae
Chain IDs:Z
Chain Length:116
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60619 Pfam ID:PF01780
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA DA A ?
OMG DA G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
OMU DA U O2'-METHYLURIDINE 5'-MONOPHOSPHATE
PSU DA U PSEUDOURIDINE-5'-MONOPHOSPHATE
UR3 DA U 3-METHYLURIDINE-5'-MONOPHOSHATE
Ligand Molecules
CD
CL
K
MG
NA
SR
TAO
Primary Citation
Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui.
Antimicrob.Agents Chemother. 53 5010 5014 (2009)
PMID: 19738021 DOI: 10.1128/AAC.00817-09

Abstact

Structures have been obtained for the complexes that triacetyloleandomycin and mycalamide A form with the large ribosomal subunit of Haloarcula marismortui. Triacetyloleandomycin binds in the nascent peptide tunnel and inhibits the activity of ribosomes by blocking the growth of the nascent peptide chain. Mycalamide A binds to the E site and inhibits protein synthesis by occupying the space normally occupied by the CCA end of E-site-bound tRNAs.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
3I55