Crystal structure of the 30S ribosome in complex with compound 1
DOI:10.2210/pdb4b3m/pdb   NDB ID: NA2604
4B3M
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 796254.88
    Molecule: 16S RIBOSOMAL RNA
    Polymer: 1 Type: rna Length: 1521
    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: 208
    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: 161
    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: 155
    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: 104
    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
    Molecule: 30S RIBOSOMAL PROTEIN S14 TYPE Z
    Polymer: 14 Type: protein Length: 60
    Chains: N
    Organism: Thermus thermophilus HB8
    Molecule: 30S RIBOSOMAL PROTEIN S15
    Polymer: 15 Type: protein Length: 88
    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: 104
    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: 92
    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: 26
    Chains: V
    Organism: Thermus thermophilus HB8
    Gene Names: rpsU TTHA1396
    UniProtKB: Protein Feature View | Search PDB | Q5SIH3  
    Molecule: 5'-R(*UP*UP*CP*AP*AP*AP)-3'
    Polymer: 22 Type: rna Length: 6
    Chains: W
    Organism: Thermus thermophilus HB8
    Molecule: 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP)-3'
    Polymer: 23 Type: rna Length: 16
    Chains: Z
    Organism: Thermus thermophilus HB8
     
  •   Structure Validation Hide

    View the full validation report  

     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 2
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 3
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 4
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 5
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 6
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 7
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 8
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 9
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 10
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 11
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 12
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 13
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 14
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 15
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 16
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 17
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 18
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 19
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 20
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 21
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 22
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 23
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    4B3R   CRYSTAL STRUCTURE OF THE 30S RIBOSOME IN COMPLEX WITH COMPOUND 31 
    4B3S   CRYSTAL STRUCTURE OF THE 30S RIBOSOME IN COMPLEX WITH COMPOUND 38 
    4B3T   CRYSTAL STRUCTURE OF THE 30S RIBOSOME IN COMPLEX WITH COMPOUND 40 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    K
    Search 
    Download 
    K K
    POTASSIUM ION
    MG
    Search 
    Download 
    MG Mg
    MAGNESIUM ION
    ON0
    Search 
    Download 
    ON0 C30 H49 N5 O14
    (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6- diamino-2,6-dideoxy-beta-L-idopyranosyl)- beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2- amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside
    ZN
    Search 
    Download 
    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:NA2604
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 generated by PISA (software)
Downloadable viewers: