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(-) Description

Title :  MOLECULAR RECOGNITION OF RNA BY NEOMYCIN AND A RESTRICTED NEOMYCIN DERIVATIVE
 
Authors :  Q. Zhao, F. Zhao, K. F. Blount, Q. Han, Y. Tor, T. Hermann
Date :  15 Jun 05  (Deposition) - 20 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ribosome, Rna, A-Site. Double Helix, Neomycin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Zhao, Q. Zhao, K. F. Blount, Q. Han, Y. Tor, T. Hermann
Molecular Recognition Of Rna By Neomycin And A Restricted Neomycin Derivative
Angew. Chem. Int. Ed. Engl. V. 44 5329 2005
PubMed-ID: 16037995  |  Reference-DOI: 10.1002/ANIE.200500903
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
    Chains: A, C
    Engineered: YES
    Fragment: RIBOSOMAL RNA A-SITE
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN ESCHERICHIA COLI (BACTERIA) EXCEPT ONE RESIDUE WAS REMOVED NEAR 3' TERMINAL
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)- 3'
    Chains: B, D
    Engineered: YES
    Fragment: RIBOSOMAL RNA A-SITE
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN ESCHERICHIA COLI (BACTERIA) EXCEPT ONE RESIDUE WAS REMOVED NEAR 5' TERMINAL
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2NMY4Ligand/IonNEOMYCIN
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NMY2Ligand/IonNEOMYCIN
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NMY2Ligand/IonNEOMYCIN

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU C:6 , G C:7 , A C:8 , A C:9 , G C:10 , U C:11 , HOH C:50 , HOH C:51 , G D:24 , U D:25 , C D:26 , A D:27 , C D:28BINDING SITE FOR RESIDUE NMY C 1
2AC2SOFTWAREU A:6 , G A:7 , A A:8 , A A:9 , G A:10 , U A:11 , G B:24 , U B:25 , C B:26 , A B:27 , C B:28BINDING SITE FOR RESIDUE NMY A 17
3AC3SOFTWAREG A:2 , C B:33 , C B:34 , U C:11 , C C:12 , C C:14 , G C:15 , G C:16 , A D:32 , C D:33 , C D:34BINDING SITE FOR RESIDUE NMY C 17
4AC4SOFTWAREU A:11 , C A:12 , C A:14 , G A:15 , G A:16 , A B:32 , C B:33 , C B:34 , G C:2 , MG C:48 , C D:33 , C D:34BINDING SITE FOR RESIDUE NMY A 18
5AC5SOFTWAREG A:2BINDING SITE FOR RESIDUE MG A 41
6AC6SOFTWARENMY A:18 , G C:2BINDING SITE FOR RESIDUE MG C 48

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A04)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A04)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A04)

(-) Exons   (0, 0)

(no "Exon" information available for 2A04)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:15
                                              
                  2a04 A  2 GUGGUGAAGUCGCGG 16
                                    11     


Chain B from PDB  Type:RNA  Length:14
                                             
                  2a04 B 21 CGCGUCACACCACC 34
                                    30    


Chain C from PDB  Type:RNA  Length:15
                                              
                  2a04 C  2 GUGGUGAAGUCGCGG 16
                                    11     


Chain D from PDB  Type:RNA  Length:14
                                             
                  2a04 D 21 CGCGUCACACCACC 34
                                    30
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2A04)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A04)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A04)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2A04)

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  2a04
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 Related Entries

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(-) Related Entries Specified in the PDB File

1zx7 1zz5