General information
PDB ID 2VQE
Title MODIFIED URIDINES WITH C5-METHYLENE SUBSTITUENTS AT THE FIRST POSITION OF THE TRNA ANTICODON STABILIZE U-G WOBBLE PAIRING DURING DECODING
PDB header RIBOSOME
Date 2008-03-13
Experimental method X-RAY DIFFRACTION
Resolution (A) 2.5
Kind rna
Organism THERMUS THERMOPHILUS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
PRIDB
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb2vqe.pdb BCDEFGHIJKLMNOPQRSTU AXY 0
Biounits:
2vqe.pdb1.pdb BCDEFGHIJKLMNOPQRSTU AXY 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_S3_C Domain P80372_120-202 1.5e-33 1 No_clan C 120 202 A   
KH_2 Domain P80372_38-111 2.1e-18 1 CL0007 C 38 111   
S4 Domain P80373_99-146 1.8e-23 1 CL0492 D 99 146 A   
Ribosomal_S5_C Domain Q5SHQ5_81-152 2e-28 1 CL0329 E 81 152 A   
Ribosomal_S5 Domain Q5SHQ5_6-70 2.6e-23 1 CL0196 E 6 70 A   
Ribosomal_S6 Domain Q5SLP8_3-92 4.7e-21 1 No_clan F 3 92 A   
Ribosomal_S7 Domain P17291_2-149 8.1e-63 1 No_clan G 2 149 A   
Ribosomal_S8 Domain A0A0M9AFS9_4-138 1.4e-49 1 No_clan H 4 138 A   
Ribosomal_S15 Domain Q5SJ76_8-88 5.1e-39 1 CL0600 O 8 88 A   
Ribosomal_S17 Domain P24321_8-75 1.7e-32 1 CL0021 Q 8 75 A   
Ribosomal_S19 Domain Q5SHP2_3-83 2.5e-36 1 No_clan S 3 81 A   
Ribosomal_S2 Family P80371_10-225 3.6e-91 1 CL0067 B 10 225 A   
Ribosomal_S4 Family P80373_3-98 3.4e-32 1 CL0492 D 3 98 A   
Ribosomal_S9 Family P62669_8-128 4.9e-44 1 CL0329 I 8 128 A   
Ribosomal_S10 Family Q5SHN7_5-99 7.5e-34 1 No_clan J 5 99 A   
Ribosomal_S11 Family P80376_17-126 1.7e-42 1 CL0267 K 17 126 A   
Ribosom_S12_S23 Family Q5SHN3_12-123 2.4e-43 1 CL0021 L 15 126 AX   
Ribosomal_S13 Family P80377_3-109 8.9e-33 1 CL0303 M 3 109 A   
Ribosomal_S14 Family A0A0N0BLP2_9-60 2.2e-23 1 No_clan N 9 60 A   
Ribosomal_S16 Family Q5SJH3_8-67 2.1e-26 1 No_clan P 8 67 A   
Ribosomal_S18 Family P80382_30-79 1.9e-22 1 No_clan R 30 79 A   
Ribosomal_S20p Family P62661_8-89 1.4e-20 1 No_clan T 8 89 A   
LUC7 Family 0.00058 0 No_clan T 9 103 A
Thx Family Q5SIH3_2-25 0.0000000000000022 1 No_clan U 2 25 A   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Alpha and beta proteins (a/b)
  Fold: Flavodoxin-like
    Superfamily: Ribosomal protein S2
      Family: Ribosomal protein S2
Ribosomal protein S2 B 7 241 A -
Class: Alpha and beta proteins (a+b)
  Fold: Alpha-L RNA-binding motif
    Superfamily: Alpha-L RNA-binding motif
      Family: Ribosomal protein S4
Ribosomal protein S4 D 2 209 A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Small subunit
30S subunit E 5 154 A -
Class: Alpha and beta proteins (a+b)
  Fold: Ferredoxin-like
    Superfamily: Ribosomal protein S6
      Family: Ribosomal protein S6
Ribosomal protein S6 F 1 101 A -
Class: All alpha proteins
  Fold: Ribosomal protein S7
    Superfamily: Ribosomal protein S7
      Family: Ribosomal protein S7
Ribosomal protein S7 G 2 156 A -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal protein S8
    Superfamily: Ribosomal protein S8
      Family: Ribosomal protein S8
Ribosomal protein S8 H 1 138 A -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal protein S5 domain 2-like
    Superfamily: Ribosomal protein S5 domain 2-like
      Family: Translational machinery components
Ribosomal protein S9 I 2 128 A -
Class: Alpha and beta proteins (a+b)
  Fold: Ferredoxin-like
    Superfamily: Ribosomal protein S10
      Family: Ribosomal protein S10
Ribosomal protein S10 J 3 100 A -
Class: Alpha and beta proteins (a/b)
  Fold: Ribonuclease H-like motif
    Superfamily: Translational machinery components
      Family: Ribosomal protein L18 and S11
Ribosomal protein S11 K 11 126 A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Ribosome complexes
70S ribosome functional complex L 5 128 AX -
Class: All alpha proteins
  Fold: S13-like H2TH domain
    Superfamily: S13-like H2TH domain
      Family: Ribosomal protein S13
Ribosomal protein S13 M 2 126 A -
Class: Small proteins
  Fold: Glucocorticoid receptor-like (DNA-binding domain)
    Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
      Family: Ribosomal protein S14
Ribosomal protein S14 N 2 61 A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Ribosome complexes
70S ribosome functional complex O 2 89 A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Ribosome complexes
70S ribosome functional complex P 1 83 A -
Class: All beta proteins
  Fold: OB-fold
    Superfamily: Nucleic acid-binding proteins
      Family: Cold shock DNA-binding domain-like
Ribosomal protein S17 Q 2 105 A -
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: Ribosomal protein S18
      Family: Ribosomal protein S18
Ribosomal protein S18 R 16 88 A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Ribosome complexes
70S ribosome functional complex S 2 81 A -
Class: All alpha proteins
  Fold: Spectrin repeat-like
    Superfamily: Ribosomal protein S20
      Family: Ribosomal protein S20
Ribosomal protein S20 T 8 106 A -
Class: Peptides
  Fold: Arg-rich RNA binding peptides
    Superfamily: 30S ribosomal protein THX
      Family: 30S ribosomal protein THX
30S ribosomal protein THX U 2 25 A -
GO terms
Protein chains: GO type: GO description:
C=1-239 C small ribosomal subunit
D=1-209 F metal ion binding
L=2-132 F tRNA binding
R=1-88 C ribosome
R=1-88 F rRNA binding
R=1-88 F structural constituent of ribosome
R=1-88 P translation
Sequences
Download file with secondary structure created by Stride  
2vqe.pdb1.pdb:   [ download sequences in FASTA format ]
B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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I (protein): 
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J (protein): 
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K (protein): 
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L (protein): 
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M (protein): 
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N (protein): 
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O (protein): 
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P (protein): 
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Q (protein): 
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R (protein): 
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S (protein): 
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T (protein): 
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U (protein): 
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A (rna): 
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X (rna): 
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Y (rna): 
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