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(-) Description

Title :  CRYSTAL STRUCTURE OF AN RNA QUADRUPLEX CONTAINING INOSINE-TETRAD
 
Authors :  B. Pan, K. Shi, M. Sundaralingam
Date :  24 Apr 06  (Deposition) - 21 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Rna Quadruplex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pan, K. Shi, M. Sundaralingam
Crystal Structure Of An Rna Quadruplex Containing Inosine Tetrad: Implications For The Roles Of Nh2 Group In Purine Tetrads.
J. Mol. Biol. V. 363 451 2006
PubMed-ID: 16978642  |  Reference-DOI: 10.1016/J.JMB.2006.08.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1K11Ligand/IonPOTASSIUM ION
2SR1Ligand/IonSTRONTIUM ION
3U335Mod. Nucleotide5-BROMO-2'-DEOXY URIDINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2SR-1Ligand/IonSTRONTIUM ION
3U332Mod. Nucleotide5-BROMO-2'-DEOXY URIDINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2SR-1Ligand/IonSTRONTIUM ION
3U333Mod. Nucleotide5-BROMO-2'-DEOXY URIDINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:5 , U A:6 , K A:302 , G B:5 , U B:6 , G C:5 , U C:6 , G D:5 , U D:6BINDING SITE FOR RESIDUE K A 301
02AC2SOFTWAREG A:4 , G A:5 , K A:301 , K A:303 , G B:4 , G B:5 , G C:4 , G C:5 , G D:4 , G D:5BINDING SITE FOR RESIDUE K A 302
03AC3SOFTWAREI A:3 , G A:4 , K A:302 , K A:304 , I B:3 , G B:4 , I C:3 , G C:4 , I D:3 , G D:4BINDING SITE FOR RESIDUE K A 303
04AC4SOFTWAREG A:2 , I A:3 , K A:303 , G B:2 , I B:3 , G C:2 , I C:3 , G D:2 , I D:3BINDING SITE FOR RESIDUE K A 304
05AC5SOFTWAREG E:2 , I E:3 , K E:306 , G F:2 , I F:3 , G G:2 , I G:3 , G H:2 , I H:3BINDING SITE FOR RESIDUE K E 305
06AC6SOFTWAREI E:3 , G E:4 , K E:305 , K E:307 , I F:3 , G F:4 , I G:3 , G G:4 , I H:3 , G H:4BINDING SITE FOR RESIDUE K E 306
07AC7SOFTWAREG E:4 , G E:5 , K E:306 , K E:308 , G F:4 , G F:5 , G G:4 , G G:5 , G H:4 , G H:5BINDING SITE FOR RESIDUE K E 307
08AC8SOFTWAREG E:5 , U E:6 , K E:307 , G F:5 , U F:6 , G G:5 , U G:6 , G H:5 , U H:6BINDING SITE FOR RESIDUE K E 308
09AC9SOFTWAREHOH E:46 , U H:6 , HOH H:27 , HOH H:40BINDING SITE FOR RESIDUE K H 309
10BC1SOFTWAREHOH A:315 , U D:6 , HOH D:322BINDING SITE FOR RESIDUE K D 312
11BC2SOFTWAREU F:6 , HOH F:18 , HOH F:186 , HOH H:81BINDING SITE FOR RESIDUE K F 313
12BC3SOFTWAREU B:6 , HOH B:63 , HOH B:132 , HOH B:175BINDING SITE FOR RESIDUE SR B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GRB)

(-) 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
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:RNA  Length:4
                                  
                   2grb A 2 GGGU 6
                            ||  
                            ||  
                            2|  
                             4  


Chain B from PDB  Type:RNA  Length:4
                                  
                   2grb B 2 GGGU 6
                            ||  
                            2|  
                             4  


Chain C from PDB  Type:DNA/RNA  Length:5
                                   
                   2grb C 1 xGGGU 6
                            |||  
                            |||  
                            1-U33
                             2|  
                              4  


Chain D from PDB  Type:DNA/RNA  Length:5
                                   
                   2grb D 1 xGGGU 6
                            |||  
                            |||  
                            1-U33
                             2|  
                              4  


Chain E from PDB  Type:DNA/RNA  Length:5
                                   
                   2grb E 1 xGGGU 6
                            |||  
                            |||  
                            1-U33
                             2|  
                              4  


Chain F from PDB  Type:DNA/RNA  Length:5
                                   
                   2grb F 1 xGGGU 6
                            |||  
                            |||  
                            1-U33
                             2|  
                              4  


Chain G from PDB  Type:DNA/RNA  Length:5
                                   
                   2grb G 1 xGGGU 6
                            |||  
                            |||  
                            1-U33
                             2|  
                              4  


Chain H from PDB  Type:RNA  Length:4
                                  
                   2grb H 2 GGGU 6
                            ||  
                            2|  
                             4
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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 2GRB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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