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The structures of Capreomycin bound to the 70S ribosome. THIS FILE CONTAINS THE 30S SUBUNIT FOR MOLECULE I
DOI:10.2210/pdb3knl/pdb   NDB ID: NA0406
3KNL
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
3KNL   3KNM   3KNN   3KNO  
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The complete entry has been assigned PDB ID 4V7M and is available for download in PDBx/mmCIF and PDBML/XML formats from the FTP archive at:
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/4v7m.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v7m.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome/antibiotic
    Structure Weight: 865470.55
    Molecule: 16S ribosomal RNA
    Polymer: 1 Type: rna Length: 1508
    Chains: A
    Organism: Thermus thermophilus HB8
    Molecule: 30S ribosomal protein S2
    Polymer: 2 Type: protein Length: 256
    Chains: B
    Organism: Thermus thermophilus HB8
    Gene Names: rpsB rps2 TTHA0861
    UniProtKB: Protein Feature View | Search PDB | P80371  
    Molecule: 30S ribosomal protein S3
    Polymer: 3 Type: protein Length: 239
    Chains: C
    Organism: Thermus thermophilus HB8
    Gene Names: rpsC rps3 TTHA1686
    UniProtKB: Protein Feature View | Search PDB | P80372  
    Molecule: 30S ribosomal protein S4
    Polymer: 4 Type: protein Length: 209
    Chains: D
    Organism: Thermus thermophilus HB8
    Gene Names: rpsD rps4 TTHA1665
    UniProtKB: Protein Feature View | Search PDB | P80373  
    Molecule: 30S ribosomal protein S5
    Polymer: 5 Type: protein Length: 162
    Chains: E
    Organism: Thermus thermophilus HB8
    Gene Names: rpsE TTHA1675
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ5  
    Molecule: 30S ribosomal protein S6
    Polymer: 6 Type: protein Length: 101
    Chains: F
    Organism: Thermus thermophilus HB8
    Gene Names: rpsF TTHA0245
    UniProtKB: Protein Feature View | Search PDB | Q5SLP8  
    Molecule: 30S ribosomal protein S7
    Polymer: 7 Type: protein Length: 156
    Chains: G
    Organism: Thermus thermophilus HB8
    Gene Names: rpsG rps7 TTHA1696
    UniProtKB: Protein Feature View | Search PDB | P17291  
    Molecule: 30S ribosomal protein S8
    Polymer: 8 Type: protein Length: 138
    Chains: H
    Organism: Thermus thermophilus HB8
    Gene Names: rpsH TTHA1678
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ2  
    Molecule: 30S ribosomal protein S9
    Polymer: 9 Type: protein Length: 128
    Chains: I
    Organism: Thermus thermophilus HB8
    Gene Names: rpsI rps9 TTHA1464
    UniProtKB: Protein Feature View | Search PDB | P80374  
    Molecule: 30S ribosomal protein S10
    Polymer: 10 Type: protein Length: 105
    Chains: J
    Organism: Thermus thermophilus HB8
    Gene Names: rpsJ TTHA1693
    UniProtKB: Protein Feature View | Search PDB | Q5SHN7  
    Molecule: 30S ribosomal protein S11
    Polymer: 11 Type: protein Length: 129
    Chains: K
    Organism: Thermus thermophilus HB8
    Gene Names: rpsK rps11 TTHA1666
    UniProtKB: Protein Feature View | Search PDB | P80376  
    Molecule: 30S ribosomal protein S12
    Polymer: 12 Type: protein Length: 132
    Chains: L
    Organism: Thermus thermophilus HB8
    Gene Names: rpsL TTHA1697
    UniProtKB: Protein Feature View | Search PDB | Q5SHN3  
    Molecule: 30S ribosomal protein S13
    Polymer: 13 Type: protein Length: 126
    Chains: M
    Organism: Thermus thermophilus HB8
    Gene Names: rpsM rps13 TTHA1667
    UniProtKB: Protein Feature View | Search PDB | P80377  
    Molecule: 30S ribosomal protein S14
    Polymer: 14 Type: protein Length: 61
    Chains: N
    Organism: Thermus thermophilus HB8
    Gene Names: rpsZ rpsN TTHA1679
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ1  
    Molecule: 30S ribosomal protein S15
    Polymer: 15 Type: protein Length: 89
    Chains: O
    Organism: Thermus thermophilus HB8
    Gene Names: rpsO TTHA1138
    UniProtKB: Protein Feature View | Search PDB | Q5SJ76  
    Molecule: 30S ribosomal protein S16
    Polymer: 16 Type: protein Length: 88
    Chains: P
    Organism: Thermus thermophilus HB8
    Gene Names: rpsP TTHA1035
    UniProtKB: Protein Feature View | Search PDB | Q5SJH3  
    Molecule: 30S ribosomal protein S17
    Polymer: 17 Type: protein Length: 105
    Chains: Q
    Organism: Thermus thermophilus HB8
    Gene Names: rpsQ TTHA1683
    UniProtKB: Protein Feature View | Search PDB | Q5SHP7  
    Molecule: 30S ribosomal protein S18
    Polymer: 18 Type: protein Length: 88
    Chains: R
    Organism: Thermus thermophilus HB8
    Gene Names: rpsR TTHA0243
    UniProtKB: Protein Feature View | Search PDB | Q5SLQ0  
    Molecule: 30S ribosomal protein S19
    Polymer: 19 Type: protein Length: 93
    Chains: S
    Organism: Thermus thermophilus HB8
    Gene Names: rpsS TTHA1688
    UniProtKB: Protein Feature View | Search PDB | Q5SHP2  
    Molecule: 30S ribosomal protein S20
    Polymer: 20 Type: protein Length: 106
    Chains: T
    Organism: Thermus thermophilus HB8
    Gene Names: rpsT rps20 TTHA1397
    UniProtKB: Protein Feature View | Search PDB | P80380  
    Molecule: 30S ribosomal protein Thx
    Polymer: 21 Type: protein Length: 27
    Chains: U
    Organism: Thermus thermophilus HB8
    Gene Names: rpsU TTHA1396
    UniProtKB: Protein Feature View | Search PDB | Q5SIH3  
    Molecule: RNA (5'-R(*AP*AP*AP*AP*AP*GP*GP*AP*AP*AP*UP*A*AP*AP*AP*AP*UP*GP*CP*AP*GP*UP*UP*CP*AP*AP*UP*CP*UP*A)-3')
    Polymer: 22 Type: rna Length: 30
    Chains: V
    Details: mRNA
    Molecule: tRNA-Gln
    Polymer: 23 Type: rna Length: 75
    Chains: W
    Details: A-site tRNA Gln
    Organism: Escherichia coli DH1
    Molecule: tRNA-Met
    Polymer: 24 Type: rna Length: 77
    Chains: X
    Details: P-site tRNA fMet
    Organism: Escherichia coli DH1
    Molecule: tRNA-Gln
    Polymer: 25 Type: rna Length: 75
    Chains: Y
    Details: E-site tRNA Gln
    Organism: Pectobacterium wasabiae WPP163
    Molecule: capreomycin IA
    Polymer: 26 Type: protein Length: 6
    Chains: Z
    Organism: Streptomyces puniceus
     
  •   Structure Validation Hide

    Download full validation report    

     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 2
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 3
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 4
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 5
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 6
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 7
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 8
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 9
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 10
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 11
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 12
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 13
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 14
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 15
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 16
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 17
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 18
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 19
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 20
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 21
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 22
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 23
    Scientific Name: Escherichia coli   Taxonomy   Expression System: Escherichia coli  
    Polymer: 24
    Scientific Name: Escherichia coli   Taxonomy   Expression System: Escherichia coli  
    Polymer: 25
    Scientific Name: Pectobacterium wasabiae wpp163   Taxonomy   Expression System: Escherichia coli  
    Polymer: 26
    Scientific Name: Streptomyces puniceus   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3KNH  The structures of viomycin bound to the 70S ribosome 
    3KNI  The structures of viomycin bound to the 70S ribosome 
    3KNJ  The structures of viomycin bound to the 70S ribosome 
    3KNK  The structures of viomycin bound to the 70S ribosome 
     
  •   Biologically Interesting Molecules (BIRD) Hide
    Identifier Image Name Type Class Chain ID  
    PRD_000193 Search  PRD_000193 Capreomycin IA Cyclic peptide Inhibitor Z
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
    Search 
    Download 
    MG Mg
    MAGNESIUM ION
    ZN
    Search 
    Download 
    ZN Zn
    ZINC ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    KBE
    Search 
    KBE C6 H14 N2 O2 LYS lPeptideLinking
    DPP
    Search 
    DPP C3 H8 N2 O2 ALA lPeptideLinking
    UAL
    Search 
    UAL C4 H7 N3 O3 glycine
    MYN
    Search 
    MYN C6 H12 N4 O2 ARG lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA0406
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (3KNL and 3KNM)