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Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome. This file contains the 50S subunit and blasticidin S molecule from the first 70S ribosome.
DOI:10.2210/pdb4l6j/pdb   NDB ID: NA2537
4L6J
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
4L6J   4L6K   4L6L   4L6M  
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Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 1451161.66
    Molecule: 23S ribosomal RNA
    Polymer: 1 Type: rna Length: 2879
    Chains: A
    Organism Thermus thermophilus HB27
    Molecule: 5S ribosomal RNA
    Polymer: 2 Type: rna Length: 119
    Chains: B
    Organism Thermus thermophilus HB27
    Molecule: 50S ribosomal protein L2
    Polymer: 3 Type: protein Length: 271
    Chains: D
    Organism Thermus thermophilus HB27
    Gene Names rplB TT_C1325
    UniProtKB:   Protein Feature View | Search PDB | Q72I07  
    Molecule: 50S ribosomal protein L3
    Polymer: 4 Type: protein Length: 204
    Chains: E
    Organism Thermus thermophilus HB27
    Gene Names rplC TT_C1328
    UniProtKB:   Protein Feature View | Search PDB | Q72I04  
    Molecule: 50S ribosomal protein L4
    Polymer: 5 Type: protein Length: 202
    Chains: F
    Organism Thermus thermophilus HB27
    Gene Names rplD TT_C1327
    UniProtKB:   Protein Feature View | Search PDB | Q72I05  
    Molecule: 50S ribosomal protein L5
    Polymer: 6 Type: protein Length: 181
    Chains: G
    Organism Thermus thermophilus HB27
    Gene Names rplE TT_C1316
    UniProtKB:   Protein Feature View | Search PDB | Q72I16  
    Molecule: 50S ribosomal protein L6
    Polymer: 7 Type: protein Length: 159
    Chains: H
    Organism Thermus thermophilus HB27
    Gene Names rplF TT_C1313
    UniProtKB:   Protein Feature View | Search PDB | Q72I19  
    Molecule: 50S ribosomal protein L9
    Polymer: 8 Type: protein Length: 145
    Chains: I
    Organism Thermus thermophilus HB27
    Gene Names rplI TT_C1743
    UniProtKB:   Protein Feature View | Search PDB | Q72GV5  
    Molecule: 50S ribosomal protein L13
    Polymer: 9 Type: protein Length: 137
    Chains: J
    Organism Thermus thermophilus HB27
    Gene Names rplM TT_C1101
    UniProtKB:   Protein Feature View | Search PDB | Q72IN1  
    Molecule: 50S ribosomal protein L14
    Polymer: 10 Type: protein Length: 122
    Chains: K
    Organism Thermus thermophilus HB27
    Gene Names rplN TT_C1318
    UniProtKB:   Protein Feature View | Search PDB | Q72I14  
    Molecule: 50S ribosomal protein L15
    Polymer: 11 Type: protein Length: 146
    Chains: L
    Organism Thermus thermophilus HB27
    Gene Names rplO TT_C1309
    UniProtKB:   Protein Feature View | Search PDB | Q72I23  
    Molecule: 50S ribosomal protein L16
    Polymer: 12 Type: protein Length: 134
    Chains: M
    Organism Thermus thermophilus HB27
    Gene Names rplP TT_C1321
    UniProtKB:   Protein Feature View | Search PDB | Q72I11  
    Molecule: 50S ribosomal protein L17
    Polymer: 13 Type: protein Length: 117
    Chains: N
    Organism Thermus thermophilus HB27
    Gene Names rplQ TT_C1299
    UniProtKB:   Protein Feature View | Search PDB | Q72I33  
    Molecule: 50S ribosomal protein L18
    Polymer: 14 Type: protein Length: 98
    Chains: O
    Organism Thermus thermophilus HB27
    Gene Names rplR TT_C1312
    UniProtKB:   Protein Feature View | Search PDB | Q72I20  
    Molecule: 50S ribosomal protein L19
    Polymer: 15 Type: protein Length: 137
    Chains: P
    Organism Thermus thermophilus HB27
    Gene Names rplS TT_C0669
    UniProtKB:   Protein Feature View | Search PDB | Q72JU9  
    Molecule: 50S ribosomal protein L20
    Polymer: 16 Type: protein Length: 117
    Chains: Q
    Organism Thermus thermophilus HB27
    Gene Names rplT TT_C0185
    UniProtKB:   Protein Feature View | Search PDB | Q72L76  
    Molecule: 50S ribosomal protein L21
    Polymer: 17 Type: protein Length: 101
    Chains: R
    Organism Thermus thermophilus HB27
    Gene Names rplU TT_C1424
    UniProtKB:   Protein Feature View | Search PDB | Q72HR2  
    Molecule: 50S ribosomal protein L22
    Polymer: 18 Type: protein Length: 112
    Chains: S
    Organism Thermus thermophilus HB27
    Gene Names rplV TT_C1323
    UniProtKB:   Protein Feature View | Search PDB | Q72I09  
    Molecule: 50S ribosomal protein L23
    Polymer: 19 Type: protein Length: 92
    Chains: T
    Organism Thermus thermophilus HB27
    Gene Names rplW TT_C1326
    UniProtKB:   Protein Feature View | Search PDB | Q72I06  
    Molecule: 50S ribosomal protein L24
    Polymer: 20 Type: protein Length: 100
    Chains: U
    Organism Thermus thermophilus HB27
    Gene Names rplX TT_C1317
    UniProtKB:   Protein Feature View | Search PDB | Q72I15  
    Molecule: 50S ribosomal protein L25
    Polymer: 21 Type: protein Length: 187
    Chains: V
    Organism Thermus thermophilus HB27
    Gene Names rplY ctc TT_C1225
    UniProtKB:   Protein Feature View | Search PDB | Q72IA7  
    Molecule: 50S ribosomal protein L27
    Polymer: 22 Type: protein Length: 76
    Chains: W
    Organism Thermus thermophilus HB27
    Gene Names rpmA TT_C1423
    UniProtKB:   Protein Feature View | Search PDB | Q72HR3  
    Molecule: 50S ribosomal protein L28
    Polymer: 23 Type: protein Length: 88
    Chains: X
    Organism Thermus thermophilus HB27
    Gene Names rpmB TT_C1964
    UniProtKB:   Protein Feature View | Search PDB | Q72G84  
    Molecule: 50S ribosomal protein L29
    Polymer: 24 Type: protein Length: 62
    Chains: Y
    Organism Thermus thermophilus HB27
    Gene Names rpmC TT_C1320
    UniProtKB:   Protein Feature View | Search PDB | Q72I12  
    Molecule: 50S ribosomal protein L30
    Polymer: 25 Type: protein Length: 59
    Chains: Z
    Organism Thermus thermophilus HB27
    Gene Names rpmD TT_C1310
    UniProtKB:   Protein Feature View | Search PDB | Q72I22  
    Molecule: 50S ribosomal protein L31
    Polymer: 26 Type: protein Length: 30
    Chains: 1
    Organism Thermus thermophilus HB27
    Gene Names rpmE TT_C0708
    UniProtKB:   Protein Feature View | Search PDB | Q72JR0  
    Molecule: 50S ribosomal protein L32
    Polymer: 27 Type: protein Length: 52
    Chains: 2
    Organism Thermus thermophilus HB27
    Gene Names rpmF rpl32 TT_C0050
    UniProtKB:   Protein Feature View | Search PDB | P62652  
    Molecule: 50S ribosomal protein L33
    Polymer: 28 Type: protein Length: 44
    Chains: 3
    Organism Thermus thermophilus HB27
    Gene Names rpmG TT_C1735
    UniProtKB:   Protein Feature View | Search PDB | Q72GW3  
    Molecule: 50S ribosomal protein L34
    Polymer: 29 Type: protein Length: 48
    Chains: 4
    Organism Thermus thermophilus HB27
    Gene Names rpmH rpl34 TTHA0446
    UniProtKB:   Protein Feature View | Search PDB | P80340  
    Molecule: 50S ribosomal protein L35
    Polymer: 30 Type: protein Length: 63
    Chains: 5
    Organism Thermus thermophilus HB27
    Gene Names rpmI TT_C0184
    UniProtKB:   Protein Feature View | Search PDB | Q72L77  
     
  •   Structure Validation Hide

    Download full validation report    

     
  •   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: Thermus thermophilus   Taxonomy    
    Polymer: 23
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 24
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 25
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 26
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 27
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 28
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 29
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 30
    Scientific Name: Thermus thermophilus   Taxonomy    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    BLS
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    BLS C17 H26 N8 O5
    BLASTICIDIN S
    MG
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    MG Mg
    MAGNESIUM ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2537
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (4L6J and 4L6K)
 
 
 
  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Svidritskiy, E.,  Korostelev, A.A.

    Deposition:   2013-06-12
    Release:   2013-07-31
    Last Modified (REVDAT):   2013-08-21
     
  •   Revision History    Hide
    Mouse over text for details
    2013-08-21
    Linkage
    2013-08-21
    Other
    2013-08-21
    Binding sites and description
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   3.40
    R-Value: 0.232 (obs.)
    R-Free: 0.268
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 211.53 α = 90.00 
    b = 454.44 β = 90.00 
    c = 620.87 γ = 90.00