Co-crystal structure of Mycalamide A Bound to the Large Ribosomal Subunit DOI:10.2210/pdb3i55/pdb   NDB ID: NA0123

3I55   Display Files  close FASTA Sequence PDB File PDB File (Header) mmCIF File mmCIF File (Header) PDBML/XML File PDBML/XML File (Header)   Download Files  close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly (gz) (A+S)   Share this Page  close Facebook Twitter LinkedIn Email Link this Page

Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Ribosome/antibiotic Structure Weight: 1495047.76 Molecule: 23S ribosomal RNA Polymer: 1 Type: rna Length: 2923 Chains: 0 Organism Haloarcula marismortui ATCC 43049 Molecule: 50S ribosomal protein L2P Polymer: 2 Type: protein Length: 240 Chains: A Organism Haloarcula marismortui Gene Names rpl2p rrnAC1608 UniProtKB:   Protein Feature View | Search PDB | P20276     Molecule: 50S ribosomal protein L3P Polymer: 3 Type: protein Length: 338 Chains: B Organism Haloarcula marismortui Gene Names rpl3p rpl3 rrnAC1611 UniProtKB:   Protein Feature View | Search PDB | P20279     Molecule: 50S ribosomal protein L4P Polymer: 4 Type: protein Length: 246 Chains: C Organism Haloarcula marismortui Gene Names rpl4p rpl4 rrnAC1610 UniProtKB:   Protein Feature View | Search PDB | P12735     Molecule: 50S ribosomal protein L5P Polymer: 5 Type: protein Length: 177 Chains: D Organism Haloarcula marismortui Gene Names rpl5p rrnAC1598 UniProtKB:   Protein Feature View | Search PDB | P14124     Molecule: 50S ribosomal protein L6P Polymer: 6 Type: protein Length: 178 Chains: E Organism Haloarcula marismortui Gene Names rpl6p rrnAC1596 UniProtKB:   Protein Feature View | Search PDB | P14135     Molecule: 50S ribosomal protein L7Ae Polymer: 7 Type: protein Length: 120 Chains: F Organism Haloarcula marismortui Gene Names rpl7ae rrnAC0103 UniProtKB:   Protein Feature View | Search PDB | P12743     Molecule: 50S ribosomal protein L10E Polymer: 8 Type: protein Length: 348 Chains: G Organism Haloarcula marismortui Gene Names rplP0 rpl10e rrnAC1417 UniProtKB:   Protein Feature View | Search PDB | P15825     Molecule: 50S ribosomal protein L10e Polymer: 9 Type: protein Length: 174 Chains: H Organism Haloarcula marismortui Gene Names rpl10e rrnAC2357 UniProtKB:   Protein Feature View | Search PDB | P60617     Molecule: 50S ribosomal protein L11P Polymer: 10 Type: protein Length: 162 Chains: I Organism Haloarcula marismortui Gene Names rpl11p rrnAC1414 UniProtKB:   Protein Feature View | Search PDB | P14122     Molecule: 50S ribosomal protein L13P Polymer: 11 Type: protein Length: 145 Chains: J Organism Haloarcula marismortui Gene Names rpl13p rrnAC0065 UniProtKB:   Protein Feature View | Search PDB | P29198     Molecule: 50S ribosomal protein L14P Polymer: 12 Type: protein Length: 132 Chains: K Organism Haloarcula marismortui Gene Names rpl14p rrnAC1602 UniProtKB:   Protein Feature View | Search PDB | P22450     Molecule: 50S ribosomal protein L15P Polymer: 13 Type: protein Length: 165 Chains: L Organism Haloarcula marismortui Gene Names rpl15p rrnAC1590 UniProtKB:   Protein Feature View | Search PDB | P12737     Molecule: 50S ribosomal protein L15e Polymer: 14 Type: protein Length: 194 Chains: M Organism Haloarcula marismortui Gene Names rpl15e rrnAC2065 UniProtKB:   Protein Feature View | Search PDB | P60618     Molecule: 50S ribosomal protein L18P Polymer: 15 Type: protein Length: 187 Chains: N Organism Haloarcula marismortui Gene Names rpl18p rrnAC1593 UniProtKB:   Protein Feature View | Search PDB | P14123     Molecule: 50S ribosomal protein L18e Polymer: 16 Type: protein Length: 116 Chains: O Organism Haloarcula marismortui Gene Names rpl18e rrnAC0064 UniProtKB:   Protein Feature View | Search PDB | P12733     Molecule: 50S ribosomal protein L19e Polymer: 17 Type: protein Length: 149 Chains: P Organism Haloarcula marismortui Gene Names rpl19e rrnAC1594 UniProtKB:   Protein Feature View | Search PDB | P14119     Molecule: 50S ribosomal protein L21e Polymer: 18 Type: protein Length: 96 Chains: Q Organism Haloarcula marismortui Gene Names rpl21e rrnAC0260 UniProtKB:   Protein Feature View | Search PDB | P12734     Molecule: 50S ribosomal protein L22P Polymer: 19 Type: protein Length: 155 Chains: R Organism Haloarcula marismortui Gene Names rpl22p rrnAC1606 UniProtKB:   Protein Feature View | Search PDB | P10970     Molecule: 50S ribosomal protein L23P Polymer: 20 Type: protein Length: 85 Chains: S Organism Haloarcula marismortui Gene Names rpl23p rrnAC1609 UniProtKB:   Protein Feature View | Search PDB | P12732     Molecule: 50S ribosomal protein L24P Polymer: 21 Type: protein Length: 120 Chains: T Organism Haloarcula marismortui Gene Names rpl24p rrnAC1601 UniProtKB:   Protein Feature View | Search PDB | P10972     Molecule: 50S ribosomal protein L24e Polymer: 22 Type: protein Length: 66 Chains: U Organism Haloarcula marismortui Gene Names rpl24e rrnAC0104 UniProtKB:   Protein Feature View | Search PDB | P14116     Molecule: 50S ribosomal protein L29P Polymer: 23 Type: protein Length: 71 Chains: V Organism Haloarcula marismortui Gene Names rpl29p rrnAC1604 UniProtKB:   Protein Feature View | Search PDB | P10971     Molecule: 50S ribosomal protein L30P Polymer: 24 Type: protein Length: 154 Chains: W Organism Haloarcula marismortui Gene Names rpl30p rrnAC1591 UniProtKB:   Protein Feature View | Search PDB | P14121     Molecule: 50S ribosomal protein L31e Polymer: 25 Type: protein Length: 92 Chains: X Organism Haloarcula marismortui Gene Names rpl31e rrnAC3113 UniProtKB:   Protein Feature View | Search PDB | P18138     Molecule: 50S ribosomal protein L32e Polymer: 26 Type: protein Length: 241 Chains: Y Organism Haloarcula marismortui Gene Names rpl32e rrnAC1595 UniProtKB:   Protein Feature View | Search PDB | P12736     Molecule: 50S ribosomal protein L37Ae Polymer: 27 Type: protein Length: 116 Chains: Z Organism Haloarcula marismortui Gene Names rpl37ae rrnAC1669 UniProtKB:   Protein Feature View | Search PDB | P60619     Molecule: 50S ribosomal protein L37e Polymer: 28 Type: protein Length: 57 Chains: 1 Organism Haloarcula marismortui Gene Names rpl37e rrnAC0797.1 UniProtKB:   Protein Feature View | Search PDB | P32410     Molecule: 50S ribosomal protein L39e Polymer: 29 Type: protein Length: 50 Chains: 2 Organism Haloarcula marismortui Gene Names rpl39e rrnAC3112 UniProtKB:   Protein Feature View | Search PDB | P22452     Molecule: 50S ribosomal protein L44E Polymer: 30 Type: protein Length: 92 Chains: 3 Organism Haloarcula marismortui Gene Names rpl44e rrnAC3514 UniProtKB:   Protein Feature View | Search PDB | P32411     Molecule: 5S ribosomal RNA Polymer: 31 Type: rna Length: 122 Chains: 9 Organism Haloarcula marismortui Molecule: DNA/RNA (5'-R(*CP*CP*(5AA)P*(2OP)P*(PO2)P*AP*CP*C)-3') Polymer: 32 Type: hybrid Length: 8 Chains: 4     Source Hide Polymer: 1 Scientific Name: Haloarcula marismortui atcc 43049   Taxonomy     Polymer: 2 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 3 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 4 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 5 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 6 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 7 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 8 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 9 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 10 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 11 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 12 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 13 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 14 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 15 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 16 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 17 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 18 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 19 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 20 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 21 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 22 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 23 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 24 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 25 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 26 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 27 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 28 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 29 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 30 Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui   Polymer: 31 Scientific Name: Haloarcula marismortui   Taxonomy     Polymer: 32 Scientific Name: Synthetic construct   Taxonomy         Related PDB Entries Hide Identifier Details 3I56  Co-crystal structure of Triacetyloleandomcyin Bound to the Large Ribosomal Subunit.      Ligand Chemical Component Hide Identifier Formula Name Interactions CD Search  Download  Cd CADMIUM ION   Ligand Explorer CL Search  Download  Cl CHLORIDE ION   Ligand Explorer K Search  Download  K POTASSIUM ION   Ligand Explorer MG Search  Download  Mg MAGNESIUM ION   Ligand Explorer MYL Search  Download  C24 H41 N O10 Mycalamide A   Ligand Explorer NA Search  Download  Na SODIUM ION   Ligand Explorer SR Search  Download  Sr STRONTIUM ION   Ligand Explorer     Modified Residues Hide Identifier Formula Parent Type 1MA Search  C11 H16 N5 O7 P A rnaLinking OMU Search  C10 H15 N2 O9 P U rnaLinking OMG Search  C11 H16 N5 O8 P G rnaLinking UR3 Search  C10 H15 N2 O9 P U rnaLinking PSU Search  C9 H13 N2 O9 P U rnaLinking 5AA Search  C12 H19 N6 O6 P DA rnaLinking 2OP Search  C3 H6 O3 nonPolymer PO2 Search  O2 P nonPolymer     External Domain Annotations Hide CATH Classification v3.4.0: 36 Domains - data from CATH   Pfam Classification: 33 Domains - data from Pfam   GO Terms: 219 Terms - data from GO      Structural Biology Knowledgebase Data Hide   Nucleic Acid Database Hide View the NDB ID associated with this structure: NA0123     Data in orange boxes are gathered from external resources (when available). 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Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors and generated by PISA (software) Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Gurel, G.,  Blaha, G.,  Steitz, T.A.,  Moore, P.B. Deposition:   2009-07-03 Release:   2010-03-09     Revision History    Hide Mouse over text for details 2011-07-13 Version format compliance     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors EDS   Resolution[Å]:   3.11 R-Value: 0.210 (work) R-Free: 0.260 Space Group: C 2 2 21 Unit Cell:   Length [Å] Angles [°] a = 211.32 α = 90.00  b = 299.65 β = 90.00  c = 574.24 γ = 90.00      Molecule of the Month Hide Ribosomal Subunits Ribosome Ricin