General information
PDB ID 1SM1
Title COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN
PDB header RIBOSOME/ANTIBIOTIC
Date 2004-03-08
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.42
Kind rna
Organism DEINOCOCCUS RADIODURANS, STREPTOMYCES GRAMINOFACIEN
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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:
pdb1sm1.pdb 12345ABCDEFGHIJKLMNOPQRSTUWXYZ 09 0
Biounits:
1sm1.pdb1.pdb 12345ABCDEFGHIJKLMNOPQRSTUWXYZ 09 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_L36 Domain Q9RSK0_2-36 1.5e-17 1 No_clan 4 2 36   
Ribosomal_L2_C Domain Q9RXJ9_126-251 1.2e-52 1 CL0107 A 126 251   
Ribosomal_L2 Domain Q9RXJ9_42-119 1.3e-32 1 CL0021 A 42 119   
Ribosomal_L5_C Domain Q9RXJ0_84-177 5.2e-40 1 No_clan D 84 177   
Ribosomal_L5 Domain Q9RXJ0_24-80 4.9e-25 1 CL0652 D 24 80   
Ribosomal_L6 Domain Q9RSL3_11-82 5.1e-19 1 No_clan E 11 82   
Ribosomal_L6 Domain Q9RSL3_90-165 1.5e-17 1 No_clan E 90 165   
Ribosomal_L9_N Domain Q9RY49_1-46 4.5e-21 1 No_clan F 1 46   
Ribosomal_L11_N Domain Q9RSS7_8-65 2.6e-28 1 No_clan G 8 65   
Ribosomal_L11 Domain Q9RSS7_70-138 1.1e-27 1 No_clan G 70 138   
Ribosomal_L14 Domain Q9RXJ2_2-133 6.8e-51 1 No_clan I 2 133   
Ribosomal_L16 Domain Q9RXJ5_7-130 2.4e-49 1 No_clan K 8 131   
Ribosomal_L22 Domain Q9RXJ7_26-129 1.6e-32 1 No_clan Q 26 129   
Ribosomal_TL5_C Domain Q9RX88_91-175 2.2e-24 1 No_clan T 91 175   
Ribosomal_L25p Domain Q9RX88_3-83 5.5e-11 1 No_clan T 3 83   
Ribosomal_L30 Domain Q9RSL0_1-51 2.1e-19 1 No_clan X 1 51   
Ribosomal_L33 Family Q9RSS4_8-54 7.5e-19 1 CL0167 1 8 54   
Ribosomal_L34 Family Q9RSH2_1-44 2.6e-25 1 No_clan 2 1 44   
Ribosomal_L35p Family Q9RSW6_2-62 1.1e-16 1 No_clan 3 2 62   
Ribosomal_L3 Family Q9RXK2_86-181 5e-16 1 CL0575 B 87 181   
Ribosomal_L4 Family Q9RXK1_19-198 2.5e-54 1 No_clan C 19 198   
Ribosomal_L13 Family Q9RXY1_39-157 8.6e-43 1 No_clan H 39 157   
Ribosomal_L27A Family Q9RSK9_26-141 4.1e-27 1 CL0588 J 26 141   
Ribosomal_L17 Family Q9RSJ5_20-116 4e-35 1 No_clan L 20 116   
Ribosomal_L18p Family Q9RSL2_4-114 9.1e-38 1 CL0267 M 4 114   
Ribosomal_L19 Family Q9RWB4_11-120 1.3e-45 1 CL0107 N 11 120   
Ribosomal_L20 Family Q9RSW7_3-109 2.4e-45 1 No_clan O 3 109   
Ribosomal_L21p Family Q9RY64_1-98 7.1e-33 1 No_clan P 1 98   
Ribosomal_L23 Family Q9RXK0_5-90 1.2e-29 1 No_clan R 5 90   
ribosomal_L24 Family Q9RXJ1_51-114 1.3e-21 1 No_clan S 51 114   
KOW Family Q9RXJ1_18-49 1e-07 1 CL0107 S 18 49   
Ribosomal_L27 Family Q9RY65_2-81 3.1e-36 1 No_clan U 2 81   
Ribosomal_L29 Family Q9RXJ4_4-59 2.1e-17 1 CL0346 W 4 59   
Ribosomal_L31 Family Q9RW44_1-64 3.9e-23 1 No_clan Y 1 64   
Ribosomal_L32p Family P49228_5-59 6e-29 1 CL0167 Z 5 59   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit 1 N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit 2 N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit 3 N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit 4 N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit A N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit B N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit C N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit D N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit E N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit F N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit G N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit H N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit I N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit J N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit K N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit L N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit M N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit N N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit O N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit P N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit Q N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit R N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit S N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit T N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit U N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit W N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit X N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit Y N/A N/A -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Large subunit
50S subunit Z N/A N/A -
GO terms
Protein chains: GO type: GO description:
1=1-55 C cytosolic large ribosomal subunit
1=1-55 C large ribosomal subunit
1=1-55 F rRNA binding
1=1-55 F structural constituent of ribosome
1=1-55 F tRNA binding
1=1-55 P ribosomal large subunit assembly
1=1-55 P translation
2=1-47 C ribosome
2=1-47 F rRNA binding
2=1-47 F structural constituent of ribosome
2=1-47 P translation
3=1-66 C cytosolic large ribosomal subunit
3=1-66 C large ribosomal subunit
3=1-66 F rRNA binding
3=1-66 F structural constituent of ribosome
3=1-66 P translation
4=1-37 C ribosome
4=1-37 F metal ion binding
4=1-37 F rRNA binding
4=1-37 F structural constituent of ribosome
4=1-37 P translation
A=1-275 C cytosolic large ribosomal subunit
A=1-275 F RNA binding
A=1-275 F rRNA binding
A=1-275 F structural constituent of ribosome
A=1-275 F transferase activity
A=1-275 P cytoplasmic translation
B=1-211 C cytosol
B=1-211 C cytosolic large ribosomal subunit
B=1-211 F rRNA binding
B=1-211 F structural constituent of ribosome
B=1-211 P translation
C=1-205 C ribosome
C=1-205 F rRNA binding
C=1-205 F structural constituent of ribosome
C=1-205 P translation
D=1-180 C cytosolic large ribosomal subunit
D=1-180 F RNA binding
D=1-180 F rRNA binding
D=1-180 F structural constituent of ribosome
D=1-180 F tRNA binding
D=1-180 P ribosomal large subunit assembly
D=1-180 P translation
E=1-185 C cytosolic large ribosomal subunit
E=1-185 F rRNA binding
E=1-185 F structural constituent of ribosome
E=1-185 P cytoplasmic translation
F=1-146 C cytosolic large ribosomal subunit
F=1-146 F rRNA binding
F=1-146 F structural constituent of ribosome
F=1-146 P translation
G=1-144 C cytosolic large ribosomal subunit
G=1-144 C large ribosomal subunit
G=1-144 C ribosome
G=1-144 F large ribosomal subunit rRNA binding
G=1-144 F rRNA binding
G=1-144 F structural constituent of ribosome
G=1-144 P ribosomal large subunit assembly
G=1-144 P translation
H=1-174 C cytosolic large ribosomal subunit
H=1-174 C ribosome
H=1-174 F mRNA binding
H=1-174 F rRNA binding
H=1-174 F structural constituent of ribosome
H=1-174 P negative regulation of translation
H=1-174 P translation
I=1-134 C cytosolic large ribosomal subunit
I=1-134 F large ribosomal subunit rRNA binding
I=1-134 F structural constituent of ribosome
I=1-134 P translation
J=1-156 C cytosolic large ribosomal subunit
J=1-156 F rRNA binding
J=1-156 F structural constituent of ribosome
J=1-156 P translation
K=1-141 C cytosolic large ribosomal subunit
K=1-141 F rRNA binding
K=1-141 F structural constituent of ribosome
K=1-141 F tRNA binding
K=1-141 P translation
L=1-116 C cytosolic large ribosomal subunit
L=1-116 C large ribosomal subunit
L=1-116 F rRNA binding
L=1-116 F structural constituent of ribosome
L=1-116 P translation
M=1-114 C cytosolic large ribosomal subunit
M=1-114 F 5S rRNA binding
M=1-114 F structural constituent of ribosome
M=1-114 P translation
N=1-166 C cytosolic large ribosomal subunit
N=1-166 F rRNA binding
N=1-166 F structural constituent of ribosome
N=1-166 P translation
O=1-118 C cytosolic large ribosomal subunit
O=1-118 F rRNA binding
O=1-118 F structural constituent of ribosome
O=1-118 P ribosomal large subunit assembly
O=1-118 P translation
P=1-100 C ribosome
P=1-100 F rRNA binding
P=1-100 F structural constituent of ribosome
P=1-100 P translation
Q=1-134 C cytosolic large ribosomal subunit
Q=1-134 C large ribosomal subunit
Q=1-134 F rRNA binding
Q=1-134 F structural constituent of ribosome
Q=1-134 P ribosome assembly
Q=1-134 P translation
R=1-95 C cytosolic large ribosomal subunit
R=1-95 F rRNA binding
R=1-95 F structural constituent of ribosome
R=1-95 P ribosomal large subunit assembly
R=1-95 P translation
S=1-115 C cytosolic large ribosomal subunit
S=1-115 F rRNA binding
S=1-115 F structural constituent of ribosome
S=1-115 P translation
T=1-237 C cytosolic large ribosomal subunit
T=1-237 F 5S rRNA binding
T=1-237 F structural constituent of ribosome
T=1-237 F tRNA binding
T=1-237 P translation
U=1-91 C cytosolic large ribosomal subunit
U=1-91 F rRNA binding
U=1-91 F structural constituent of ribosome
U=1-91 F tRNA binding
U=1-91 P translation
W=1-67 C cytosolic large ribosomal subunit
W=1-67 F rRNA binding
W=1-67 F structural constituent of ribosome
W=1-67 P translation
X=1-55 C cytosolic large ribosomal subunit
X=1-55 F rRNA binding
X=1-55 F structural constituent of ribosome
X=1-55 P translation
Y=1-73 C ribosome
Y=1-73 F rRNA binding
Y=1-73 F structural constituent of ribosome
Y=1-73 F tRNA binding
Y=1-73 P translation
Z=1-60 C large ribosomal subunit
Z=1-60 F metal ion binding
Z=1-60 F rRNA binding
Z=1-60 F structural constituent of ribosome
Z=1-60 P translation
Sequences
Download file with secondary structure created by Stride  
1sm1.pdb1.pdb:   [ download sequences in FASTA format ]
1 (protein): 
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2 (protein): 
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3 (protein): 
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4 (protein): 
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5 (protein): 
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A (protein): 
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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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W (protein): 
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X (protein): 
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Y (protein): 
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Z (protein): 
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0 (rna): 
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9 (rna): 
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