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Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.
DOI:10.2210/pdb2qb9/pdb   NDB ID: RR0173
2QB9
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
2QB9   2QBA   2QBB   2QBC  
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The complete entry has been assigned PDB ID 4V53 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/4v53.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v53.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 790219.32
    Molecule: 16S rRNA
    Polymer: 1 Type: rna Length: 1542
    Chains: A
    Organism: Escherichia coli
    Molecule: 30S ribosomal protein S3
    Polymer: 2 Type: protein Length: 232
    Chains: C
    Organism: Escherichia coli
    Gene Names: rpsC b3314 JW3276
    UniProtKB: Protein Feature View | Search PDB | P0A7V3  
    Molecule: 30S ribosomal protein S4
    Polymer: 3 Type: protein Length: 205
    Chains: D
    Organism: Escherichia coli
    Gene Names: rpsD ramA b3296 JW3258
    UniProtKB: Protein Feature View | Search PDB | P0A7V8  
    Molecule: 30S ribosomal protein S5
    Polymer: 4 Type: protein Length: 166
    Chains: E
    Organism: Escherichia coli
    Gene Names: rpsE spc b3303 JW3265
    UniProtKB: Protein Feature View | Search PDB | P0A7W1  
    Molecule: 30S ribosomal protein S6
    Polymer: 5 Type: protein Length: 135
    Chains: F
    Organism: Escherichia coli
    Gene Names: rpsF b4200 JW4158
    UniProtKB: Protein Feature View | Search PDB | P02358  
    Molecule: 30S ribosomal protein S7
    Polymer: 6 Type: protein Length: 178
    Chains: G
    Organism: Escherichia coli
    Gene Names: rpsG b3341 JW3303
    UniProtKB: Protein Feature View | Search PDB | P02359  
    Molecule: 30S ribosomal protein S8
    Polymer: 7 Type: protein Length: 129
    Chains: H
    Organism: Escherichia coli
    Gene Names: rpsH b3306 JW3268
    UniProtKB: Protein Feature View | Search PDB | P0A7W7  
    Molecule: 30S ribosomal protein S9
    Polymer: 8 Type: protein Length: 129
    Chains: I
    Organism: Escherichia coli
    Gene Names: rpsI b3230 JW3199
    UniProtKB: Protein Feature View | Search PDB | P0A7X3  
    Molecule: 30S ribosomal protein S10
    Polymer: 9 Type: protein Length: 103
    Chains: J
    Organism: Escherichia coli
    Gene Names: rpsJ nusE b3321 JW3283
    UniProtKB: Protein Feature View | Search PDB | P0A7R5  
    Molecule: 30S ribosomal protein S11
    Polymer: 10 Type: protein Length: 128
    Chains: K
    Organism: Escherichia coli
    Gene Names: rpsK b3297 JW3259
    UniProtKB: Protein Feature View | Search PDB | P0A7R9  
    Molecule: 30S ribosomal protein S12
    Polymer: 11 Type: protein Length: 123
    Chains: L
    Organism: Escherichia coli
    Gene Names: rpsL strA b3342 JW3304
    UniProtKB: Protein Feature View | Search PDB | P0A7S3  
    Molecule: 30S ribosomal protein S13
    Polymer: 12 Type: protein Length: 117
    Chains: M
    Organism: Escherichia coli
    Gene Names: rpsM b3298 JW3260
    UniProtKB: Protein Feature View | Search PDB | P0A7S9  
    Molecule: 30S ribosomal protein S14
    Polymer: 13 Type: protein Length: 100
    Chains: N
    Organism: Escherichia coli
    Gene Names: rpsN b3307 JW3269
    UniProtKB: Protein Feature View | Search PDB | P0AG59  
    Molecule: 30S ribosomal protein S15
    Polymer: 14 Type: protein Length: 89
    Chains: O
    Organism: Escherichia coli
    Gene Names: rpsO secC b3165 JW3134
    UniProtKB: Protein Feature View | Search PDB | P0ADZ4  
    Molecule: 30S ribosomal protein S16
    Polymer: 15 Type: protein Length: 82
    Chains: P
    Organism: Escherichia coli
    Gene Names: rpsP b2609 JW2590
    UniProtKB: Protein Feature View | Search PDB | P0A7T3  
    Molecule: 30S ribosomal protein S17
    Polymer: 16 Type: protein Length: 83
    Chains: Q
    Organism: Escherichia coli
    Gene Names: rpsQ neaA b3311 JW3273
    UniProtKB: Protein Feature View | Search PDB | P0AG63  
    Molecule: 30S ribosomal protein S18
    Polymer: 17 Type: protein Length: 74
    Chains: R
    Organism: Escherichia coli
    Gene Names: rpsR b4202 JW4160
    UniProtKB: Protein Feature View | Search PDB | P0A7T7  
    Molecule: 30S ribosomal protein S19
    Polymer: 18 Type: protein Length: 91
    Chains: S
    Organism: Escherichia coli
    Gene Names: rpsS b3316 JW3278
    UniProtKB: Protein Feature View | Search PDB | P0A7U3  
    Molecule: 30S ribosomal protein S20
    Polymer: 19 Type: protein Length: 86
    Chains: T
    Organism: Escherichia coli
    Gene Names: rpsT b0023 JW0022
    UniProtKB: Protein Feature View | Search PDB | P0A7U7  
    Molecule: 30S ribosomal protein S2
    Polymer: 20 Type: protein Length: 240
    Chains: B
    Organism: Escherichia coli
    Gene Names: rpsB b0169 JW0164
    UniProtKB: Protein Feature View | Search PDB | P0A7V0  
    Molecule: 30S ribosomal protein S21
    Polymer: 21 Type: protein Length: 70
    Chains: U
    Organism: Escherichia coli
    Gene Names: rpsU b3065 JW3037
    UniProtKB: Protein Feature View | Search PDB | P68679  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 2
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 3
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 4
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 5
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 6
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 7
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 8
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 9
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 10
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 11
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 12
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 13
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 14
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 15
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 16
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 17
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 18
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 19
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 20
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 21
    Scientific Name: Escherichia coli   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    2QBA  50s subunit of 70s ribosome one 
    2QBB  30s subunit of 70s ribosome two 
    2QBC  50s subunit of 70s ribosome two 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    LLL
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    LLL C19 H39 N5 O7
    (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO- 3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO- 2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)- 5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN- 3,5-DIOL
    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: RR0173
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (2QB9 and 2QBA)