General information
PDB ID 2RDO
Title 50S SUBUNIT WITH EF-G(GDPNP) AND RRF BOUND
PDB header RIBOSOME
Date 2007-09-24
Experimental method ELECTRON MICROSCOPY
Resolution (A) 9.1
Kind rna
Organism ESCHERICHIA COLI
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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:
pdb2rdo.pdb VCDEFGJKLMNOPQRSTUWXYZ01234IH978 AB 0
Biounits:
2rdo.pdb1.pdb VCDEFGJKLMNOPQRSTUWXYZ01234IH978 AB 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_L36 Domain P0A7Q6_1-38 2.3e-20 1 No_clan 4 1 38   
GTP_EFTU Domain P0A6M8_8-288 1.3e-50 1 CL0023 7 8 288   
EFG_IV Domain P0A6M8_486-609 1.7e-45 1 CL0329 7 486 609   
EFG_II Domain P0A6M8_411-485 1e-33 1 CL0437 7 411 485   
EFG_C Domain P0A6M8_611-698 8e-29 1 CL0437 7 611 698   
GTP_EFTU_D2 Domain P0A6M8_331-398 5e-16 1 CL0575 7 331 398   
RRF Domain P0A805_20-183 2.7e-63 1 No_clan 8 20 183   
Ribosomal_L1 Domain P0A7L0_30-220 4.2e-52 1 No_clan 9 29 219   
Ribosomal_L2_C Domain P60422_125-249 9.2e-56 1 CL0107 C 124 248   
Ribosomal_L2 Domain P60422_42-118 7.6e-34 1 CL0021 C 41 117   
Ribosomal_L5_C Domain P62399_84-177 5.3e-41 1 No_clan F 83 176   
Ribosomal_L5 Domain P62399_24-80 9.8e-29 1 CL0652 F 23 79   
Ribosomal_L6 Domain P0AG55_90-165 7e-19 1 No_clan G 89 164   
Ribosomal_L6 Domain P0AG55_11-82 1e-18 1 No_clan G 10 81   
Ribosomal_L9_C Domain P0A7R1_63-148 2.1e-25 1 No_clan H 63 148   
Ribosomal_L9_N Domain P0A7R1_1-47 3.1e-22 1 No_clan H 1 47   
Ribosomal_L11_N Domain P0A7J7_2-67 1.2e-29 1 No_clan I 8 66   
Ribosomal_L11 Domain P0A7J7_72-140 4.4e-24 1 No_clan I 71 139   
Ribosomal_L14 Domain P0ADY3_2-122 2.1e-53 1 No_clan K 2 122   
Ribosomal_L22 Domain P61175_5-108 7.6e-38 1 No_clan S 5 108   
Ribosomal_L25p Domain P68919_4-91 2.7e-25 1 No_clan V 4 91   
Ribosomal_L30 Domain P0AG51_5-55 2.7e-19 1 No_clan Y 4 54   
Ribosomal_L32p Family P0A7N4_2-57 1.8e-19 1 CL0167 0 1 56   
Ribosomal_L33 Family P0A7N9_7-53 8.3e-19 1 CL0167 1 6 52   
Ribosomal_L34 Family P0A7P5_1-44 1.7e-24 1 No_clan 2 1 44   
Ribosomal_L35p Family P0A7Q1_2-62 2.4e-22 1 No_clan 3 1 61   
Ribosomal_L3 Family P60438_4-185 0.00000000000001 1 CL0575 D 4 185   
Ribosomal_L4 Family P60723_12-199 3.1e-64 1 No_clan E 12 199   
Ribosomal_L13 Family P0AA10_14-138 4.7e-57 1 No_clan J 14 138   
Ribosomal_L27A Family P02413_27-144 3.4e-32 1 CL0588 L 27 144   
Ribosomal_L16 Family P0ADY7_4-131 2.8e-47 1 No_clan M 4 131   
Ribosomal_L17 Family P0AG44_20-116 1.3e-34 1 No_clan N 20 116   
Ribosomal_L18p Family P0C018_1-117 7.7e-44 1 CL0267 O 1 117   
Ribosomal_L19 Family P0A7K6_3-113 4.4e-50 1 CL0107 P 2 112   
Ribosomal_L20 Family P0A7L3_3-109 5.1e-49 1 No_clan Q 2 108   
Ribosomal_L21p Family P0AG48_1-101 1.3e-37 1 No_clan R 1 101   
Ribosomal_L23 Family P0ADZ0_9-95 4.3e-31 1 No_clan T 9 95   
ribosomal_L24 Family P60624_39-103 1.6e-23 1 No_clan U 38 102   
KOW Family P60624_7-37 0.000074 1 CL0107 U 6 36   
Ribosomal_L27 Family P0A7L8_2-82 6.1e-39 1 No_clan W 1 81   
Ribosomal_L29 Family P0A7M6_4-60 6.4e-23 1 CL0346 X 4 60   
Ribosomal_L31 Family P0A7M9_1-65 7.5e-31 1 No_clan Z 1 65   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Small proteins
  Fold: Rubredoxin-like
    Superfamily: Zn-binding ribosomal proteins
      Family: Ribosomal protein L32p
Ribosomal protein L32p 0 1 56 -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Ribosome complexes
70S ribosome functional complex 1 3 52 -
Class: Alpha and beta proteins (a+b)
  Fold: L35p-like
    Superfamily: L35p-like
      Family: Ribosomal protein L35p
Ribosomal protein L35p 3 1 64 -
Class: Small proteins
  Fold: Ribosomal protein L36
    Superfamily: Ribosomal protein L36
      Family: Ribosomal protein L36
Ribosomal protein L36 4 1 38 -
Class: Alpha and beta proteins (a+b)
  Fold: RRF/tRNA synthetase additional domain-like
    Superfamily: Ribosome recycling factor, RRF
      Family: Ribosome recycling factor, RRF
Ribosome recycling factor, RRF 8 1 185 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: Translation proteins SH3-like domain
      Family: C-terminal domain of ribosomal protein L2
C-terminal domain of ribosomal protein L2 C 125 269 -
Class: All beta proteins
  Fold: OB-fold
    Superfamily: Nucleic acid-binding proteins
      Family: Cold shock DNA-binding domain-like
N-terminal domain of ribosomal protein L2 C 61 124 -
Class: All beta proteins
  Fold: Reductase/isomerase/elongation factor common domain
    Superfamily: Translation proteins
      Family: Ribosomal protein L3
Ribosomal protein L3 D 1 209 -
Class: Alpha and beta proteins (a/b)
  Fold: Ribosomal protein L4
    Superfamily: Ribosomal protein L4
      Family: Ribosomal protein L4
Ribosomal protein L4 E 1 201 -
Class: Alpha and beta proteins (a+b)
  Fold: RL5-like
    Superfamily: RL5-like
      Family: Ribosomal protein L5
Ribosomal protein L5 F 1 178 -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal protein L6
    Superfamily: Ribosomal protein L6
      Family: Ribosomal protein L6
Ribosomal protein L6 G 1 81 -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal protein L6
    Superfamily: Ribosomal protein L6
      Family: Ribosomal protein L6
Ribosomal protein L6 G 82 176 -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal protein L9 C-domain
    Superfamily: Ribosomal protein L9 C-domain
      Family: Ribosomal protein L9 C-domain
Ribosomal protein L9 C-domain H 59 149 -
Class: Alpha and beta proteins (a+b)
  Fold: MbtH/L9 domain-like
    Superfamily: L9 N-domain-like
      Family: Ribosomal protein L9 N-domain
Ribosomal protein L9 N-domain H 1 58 -
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: Ribosomal protein L11, C-terminal domain
      Family: Ribosomal protein L11, C-terminal domain
Ribosomal protein L11, C-terminal domain I 73 141 -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal L11/L12e N-terminal domain
    Superfamily: Ribosomal L11/L12e N-terminal domain
      Family: Ribosomal L11/L12e N-terminal domain
Ribosomal protein L11, N-terminal domain I 1 72 -
Class: Alpha and beta proteins (a/b)
  Fold: Ribosomal protein L13
    Superfamily: Ribosomal protein L13
      Family: Ribosomal protein L13
Ribosomal protein L13 J 1 140 -
Class: All beta proteins
  Fold: Ribosomal protein L14
    Superfamily: Ribosomal protein L14
      Family: Ribosomal protein L14
Ribosomal protein L14 K 2 122 -
Class: Alpha and beta proteins (a/b)
  Fold: Ribosomal proteins L15p and L18e
    Superfamily: Ribosomal proteins L15p and L18e
      Family: Ribosomal proteins L15p and L18e
Ribosomal protein L15 (L15p) L 2 144 -
Class: Alpha and beta proteins (a+b)
  Fold: alpha/beta-Hammerhead
    Superfamily: Ribosomal protein L16p/L10e
      Family: Ribosomal protein L16p
Ribosomal protein L16p M 1 136 -
Class: Alpha and beta proteins (a+b)
  Fold: Prokaryotic ribosomal protein L17
    Superfamily: Prokaryotic ribosomal protein L17
      Family: Prokaryotic ribosomal protein L17
Prokaryotic ribosomal protein L17 N 1 127 -
Class: Alpha and beta proteins (a/b)
  Fold: Ribonuclease H-like motif
    Superfamily: Translational machinery components
      Family: Ribosomal protein L18 and S11
Ribosomal protein L18 (L18p) O 1 117 -
Class: Low resolution protein structures
  Fold: Ribosome and ribosomal fragments
    Superfamily: Ribosome and ribosomal fragments
      Family: Ribosome complexes
70S ribosome functional complex P 1 114 -
Class: All alpha proteins
  Fold: PABP domain-like
    Superfamily: Ribosomal protein L20
      Family: Ribosomal protein L20
Ribosomal protein L20 Q 1 117 -
Class: All beta proteins
  Fold: L21p-like
    Superfamily: L21p-like
      Family: Ribosomal protein L21p
Ribosomal protein L21p R 1 103 -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal protein L22
    Superfamily: Ribosomal protein L22
      Family: Ribosomal protein L22
Ribosomal protein L22 S 1 110 -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal proteins S24e, L23 and L15e
    Superfamily: Ribosomal proteins S24e, L23 and L15e
      Family: L23p
Ribosomal protein L23 T 1 99 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: Translation proteins SH3-like domain
      Family: Ribosomal proteins L24p and L21e
Ribosomal proteins L24 (L24p) U 1 102 -
Class: All beta proteins
  Fold: Ribosomal protein L25-like
    Superfamily: Ribosomal protein L25-like
      Family: Ribosomal protein L25-like
Ribosomal protein L25 V 1 94 -
Class: All beta proteins
  Fold: Barrel-sandwich hybrid
    Superfamily: Ribosomal L27 protein-like
      Family: Ribosomal L27 protein
Ribosomal protein L27 W 1 84 -
Class: All alpha proteins
  Fold: Long alpha-hairpin
    Superfamily: Ribosomal protein L29 (L29p)
      Family: Ribosomal protein L29 (L29p)
Ribosomal protein L29 (L29p) X 1 63 -
Class: Alpha and beta proteins (a+b)
  Fold: Ribosomal protein L30p/L7e
    Superfamily: Ribosomal protein L30p/L7e
      Family: Ribosomal protein L30p/L7e
Prokaryotic ribosomal protein L30 Y 1 58 -
Class: Alpha and beta proteins (a+b)
  Fold: L28p-like
    Superfamily: L28p-like
      Family: Ribosomal protein L31p
Ribosomal protein L31p Z 1 70 -
GO terms
Protein chains: GO type: GO description:
3=2-65 C cytosolic large ribosomal subunit
3=2-65 F structural constituent of ribosome
3=2-65 P translation
7=1-704 F GTPase activity
7=1-704 F translation elongation factor activity
7=1-704 F GTP binding
7=1-704 P GTP catabolic process
8=1-185 C cytoplasm
9=2-234 P negative regulation of translational initiation
C=2-273 F transferase activity
E=1-201 P regulation of translation
E=1-201 P regulation of transcription, DNA-dependent
E=1-201 P DNA-dependent transcription, termination
F=2-179 F tRNA binding
G=2-177 C ribosome
G=2-177 F rRNA binding
G=2-177 P response to antibiotic
I=2-142 P stringent response
I=2-142 P translational termination
J=1-142 F zinc ion binding
Q=2-118 F translation repressor activity, nucleic acid binding
Q=2-118 P ribosomal large subunit assembly
S=1-110 C large ribosomal subunit
T=1-100 F nucleotide binding
V=1-94 F 5S rRNA binding
Sequences
Download file with secondary structure created by Stride  
2rdo.pdb1.pdb:   [ download sequences in FASTA format ]
0 (protein): 
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1 (protein): 
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2 (protein): 
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3 (protein): 
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4 (protein): 
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7 (protein): 
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8 (protein): 
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9 (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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V (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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A (rna): 
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B (rna): 
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