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(-) Description

Title :  CRYSTAL STRUCTURE OF AN RNA DUPLEX WITH URIDINE BULGES
 
Authors :  Y. Xiong, J. Deng, C. Sudarsanakumar, M. Sundaralingam
Date :  25 May 01  (Deposition) - 26 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Uridine Bulge, Rna Duplex, A-Form, Kink, Metal Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Xiong, J. Deng, C. Sudarsanakumar, M. Sundaralingam
Crystal Structure Of An Rna Duplex R(Gugucgcac)(2) With Uridine Bulges.
J. Mol. Biol. V. 313 573 2001
PubMed-ID: 11676540  |  Reference-DOI: 10.1006/JMBI.2001.5045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
    Chains: A, B, C, D
    Engineered: YES
    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, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CBR4Mod. Nucleotide5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CBR2Mod. Nucleotide5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CBR2Mod. Nucleotide5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:118 , U C:22 , C C:23 , HOH C:110 , HOH C:141 , C D:36BINDING SITE FOR RESIDUE CA C 101
2AC2SOFTWAREC C:27 , HOH C:119 , U D:31 , C D:32 , HOH D:132 , HOH D:139BINDING SITE FOR RESIDUE CA D 102
3AC3SOFTWAREU A:4 , C A:5 , HOH A:179 , HOH A:234 , C B:18 , HOH D:182 , HOH D:238BINDING SITE FOR RESIDUE CA A 103
4AC4SOFTWAREC A:9 , HOH A:196 , U B:13 , C B:14 , HOH B:163 , HOH B:252BINDING SITE FOR RESIDUE CA B 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J9H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J9H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J9H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J9H)

(-) Exons   (0, 0)

(no "Exon" information available for 1J9H)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:DNA/RNA  Length:9
                                        
                  1j9h A  1 GUGUCGcAC  9
                                  |  
                                  7-CBR


Chain B from PDB  Type:DNA/RNA  Length:9
                                        
                  1j9h B 10 GUGUCGcAC 18
                                  |  
                                 16-CBR


Chain C from PDB  Type:DNA/RNA  Length:9
                                        
                  1j9h C 19 GUGUCGcAC 27
                                  |  
                                 25-CBR


Chain D from PDB  Type:DNA/RNA  Length:9
                                        
                  1j9h D 28 GUGUCGcAC 36
                                  |  
                                 34-CBR
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1J9H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1J9H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J9H)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1J9H)

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  1j9h
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