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Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 50S 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/pdb2qba/pdb   NDB ID: RR0174
2QBA
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
2QB9   2QBA   2QBB   2QBC  
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Primary Citation
 
 
  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 1359176.50
    Molecule: 5S rRNA
    Polymer: 1 Type: rna Length: 120
    Chains: A
    Organism Escherichia coli
    Molecule: 23S rRNA
    Polymer: 2 Type: rna Length: 2904
    Chains: B
    Organism Escherichia coli
    Molecule: 50S ribosomal protein L11
    Polymer: 3 Type: protein Length: 141
    Chains: I
    Organism Escherichia coli
    Gene Names rplK relC b3983 JW3946
    UniProtKB:   Protein Feature View | Search PDB | P0A7J7  
    Molecule: 50S ribosomal protein L2
    Polymer: 4 Type: protein Length: 272
    Chains: C
    Organism Escherichia coli
    Gene Names rplB b3317 JW3279
    UniProtKB:   Protein Feature View | Search PDB | P60422  
    Molecule: 50S ribosomal protein L3
    Polymer: 5 Type: protein Length: 209
    Chains: D
    Organism Escherichia coli
    Gene Names rplC b3320 JW3282
    UniProtKB:   Protein Feature View | Search PDB | P60438  
    Molecule: 50S ribosomal protein L14
    Polymer: 6 Type: protein Length: 123
    Chains: K
    Organism Escherichia coli
    Gene Names rplN b3310 JW3272
    UniProtKB:   Protein Feature View | Search PDB | P0ADY3  
    Molecule: 50S ribosomal protein L19
    Polymer: 7 Type: protein Length: 114
    Chains: P
    Organism Escherichia coli
    Gene Names rplS b2606 JW2587
    UniProtKB:   Protein Feature View | Search PDB | P0A7K6  
    Molecule: 50S ribosomal protein L4
    Polymer: 8 Type: protein Length: 201
    Chains: E
    Organism Escherichia coli
    Gene Names rplD eryA b3319 JW3281
    UniProtKB:   Protein Feature View | Search PDB | P60723  
    Molecule: 50S ribosomal protein L30
    Polymer: 9 Type: protein Length: 58
    Chains: Y
    Organism Escherichia coli
    Gene Names rpmD b3302 JW3264
    UniProtKB:   Protein Feature View | Search PDB | P0AG51  
    Molecule: 50S ribosomal protein L32
    Polymer: 10 Type: protein Length: 56
    Chains: 0
    Organism Escherichia coli
    Gene Names rpmF b1089 JW1075
    UniProtKB:   Protein Feature View | Search PDB | P0A7N4  
    Molecule: 50S ribosomal protein L36
    Polymer: 11 Type: protein Length: 38
    Chains: 4
    Organism Escherichia coli
    Gene Names rpmJ b3299 JW3261
    UniProtKB:   Protein Feature View | Search PDB | P0A7Q6  
    Molecule: 50S ribosomal protein L33
    Polymer: 12 Type: protein Length: 54
    Chains: 1
    Organism Escherichia coli
    Gene Names rpmG b3636 JW3611
    UniProtKB:   Protein Feature View | Search PDB | P0A7N9  
    Molecule: 50S ribosomal protein L35
    Polymer: 13 Type: protein Length: 64
    Chains: 3
    Organism Escherichia coli
    Gene Names rpmI b1717 JW1707
    UniProtKB:   Protein Feature View | Search PDB | P0A7Q1  
    Molecule: 50S ribosomal protein L25
    Polymer: 14 Type: protein Length: 94
    Chains: V
    Organism Escherichia coli
    Gene Names rplY b2185 JW2173
    UniProtKB:   Protein Feature View | Search PDB | P68919  
    Molecule: 50S ribosomal protein L34
    Polymer: 15 Type: protein Length: 46
    Chains: 2
    Organism Escherichia coli
    Gene Names rpmH rimA ssaF b3703 JW3680
    UniProtKB:   Protein Feature View | Search PDB | P0A7P5  
    Molecule: 50S ribosomal protein L15
    Polymer: 16 Type: protein Length: 144
    Chains: L
    Organism Escherichia coli
    Gene Names rplO b3301 JW3263
    UniProtKB:   Protein Feature View | Search PDB | P02413  
    Molecule: 50S ribosomal protein L16
    Polymer: 17 Type: protein Length: 136
    Chains: M
    Organism Escherichia coli
    Gene Names rplP b3313 JW3275
    UniProtKB:   Protein Feature View | Search PDB | P0ADY7  
    Molecule: 50S ribosomal protein L29
    Polymer: 18 Type: protein Length: 63
    Chains: X
    Organism Escherichia coli
    Gene Names rpmC b3312 JW3274
    UniProtKB:   Protein Feature View | Search PDB | P0A7M6  
    Molecule: 50S ribosomal protein L9
    Polymer: 19 Type: protein Length: 149
    Chains: H
    Organism Escherichia coli
    Gene Names rplI b4203 JW4161
    UniProtKB:   Protein Feature View | Search PDB | P0A7R1  
    Molecule: 50S ribosomal protein L13
    Polymer: 20 Type: protein Length: 142
    Chains: J
    Organism Escherichia coli
    Gene Names rplM b3231 JW3200
    UniProtKB:   Protein Feature View | Search PDB | P0AA10  
    Molecule: 50S ribosomal protein L17
    Polymer: 21 Type: protein Length: 127
    Chains: N
    Organism Escherichia coli
    Gene Names rplQ b3294 JW3256
    UniProtKB:   Protein Feature View | Search PDB | P0AG44  
    Molecule: 50S ribosomal protein L18
    Polymer: 22 Type: protein Length: 117
    Chains: O
    Organism Escherichia coli
    Gene Names rplR b3304 JW3266
    UniProtKB:   Protein Feature View | Search PDB | P0C018  
    Molecule: 50S ribosomal protein L20
    Polymer: 23 Type: protein Length: 117
    Chains: Q
    Organism Escherichia coli
    Gene Names rplT pdzA b1716 JW1706
    UniProtKB:   Protein Feature View | Search PDB | P0A7L3  
    Molecule: 50S ribosomal protein L22
    Polymer: 24 Type: protein Length: 110
    Chains: S
    Organism Escherichia coli
    Gene Names rplV eryB b3315 JW3277
    UniProtKB:   Protein Feature View | Search PDB | P61175  
    Molecule: 50S ribosomal protein L24
    Polymer: 25 Type: protein Length: 103
    Chains: U
    Organism Escherichia coli
    Gene Names rplX b3309 JW3271
    UniProtKB:   Protein Feature View | Search PDB | P60624  
    Molecule: 50S ribosomal protein L5
    Polymer: 26 Type: protein Length: 178
    Chains: F
    Organism Escherichia coli
    Gene Names rplE b3308 JW3270
    UniProtKB:   Protein Feature View | Search PDB | P62399  
    Molecule: 50S ribosomal protein L6
    Polymer: 27 Type: protein Length: 176
    Chains: G
    Organism Escherichia coli
    Gene Names rplF b3305 JW3267
    UniProtKB:   Protein Feature View | Search PDB | P0AG55  
    Molecule: 50S ribosomal protein L21
    Polymer: 28 Type: protein Length: 103
    Chains: R
    Organism Escherichia coli
    Gene Names rplU b3186 JW3153
    UniProtKB:   Protein Feature View | Search PDB | P0AG48  
    Molecule: 50S ribosomal protein L23
    Polymer: 29 Type: protein Length: 100
    Chains: T
    Organism Escherichia coli
    Gene Names rplW b3318 JW3280
    UniProtKB:   Protein Feature View | Search PDB | P0ADZ0  
    Molecule: 50S ribosomal protein L28
    Polymer: 30 Type: protein Length: 78
    Chains: Z
    Organism Escherichia coli
    Gene Names rpmB b3637 JW3612
    UniProtKB:   Protein Feature View | Search PDB | P0A7M2  
    Molecule: 50S ribosomal protein L27
    Polymer: 31 Type: protein Length: 84
    Chains: W
    Organism Escherichia coli
    Gene Names rpmA b3185 JW3152
    UniProtKB:   Protein Feature View | Search PDB | P0A7L8  
     
  •   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    
    Polymer: 22
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 23
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 24
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 25
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 26
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 27
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 28
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 29
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 30
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 31
    Scientific Name: Escherichia coli   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    2QB9  30s 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 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
    ZN
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    ZN Zn
    ZINC ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: RR0174
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (2QB9 and 2QBA)