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(-) Description

Title :  STRUCTURE OF A BIPYRIDINE-MODIFIED PNA DUPLEX
 
Authors :  J. I. Yeh, E. Pohl, D. Truan, W. He, G. M. Sheldrick, S. Du, Achim C.
Date :  26 Mar 10  (Deposition) - 30 Mar 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Bipyridine, Peptide Nucleic Acid, Pna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Yeh, E. Pohl, D. Truan, W. He, G. M. Sheldrick, S. Du, C. Achim
The Crystal Structure Of Non-Modified And Bipyridine-Modified Pna Duplexes.
Chemistry V. 16 11867 2010
PubMed-ID: 20859960  |  Reference-DOI: 10.1002/CHEM.201000392

(-) Compounds

Molecule 1 - BIPYRIDINE-PNA
    Chains: A, B, C, D
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESISED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 46)

Asymmetric Unit (10, 46)
No.NameCountTypeFull Name
1APN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CO32Ligand/IonCARBONATE ION
3CPN12Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
4EDO1Ligand/Ion1,2-ETHANEDIOL
5GOL2Ligand/IonGLYCEROL
6GPN12Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
7KPN4Mod. Amino AcidN-(2-AMINOETHYL)-N-(2,2'-BIPYRIDIN-5-YLACETYL)GLYCINE
8PGO2Ligand/IonS-1,2-PROPANEDIOL
9PGR3Ligand/IonR-1,2-PROPANEDIOL
10TPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
Biological Unit 1 (7, 11)
No.NameCountTypeFull Name
1APN1Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CO3-1Ligand/IonCARBONATE ION
3CPN3Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
4EDO1Ligand/Ion1,2-ETHANEDIOL
5GOL-1Ligand/IonGLYCEROL
6GPN3Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
7KPN1Mod. Amino AcidN-(2-AMINOETHYL)-N-(2,2'-BIPYRIDIN-5-YLACETYL)GLYCINE
8PGO-1Ligand/IonS-1,2-PROPANEDIOL
9PGR1Ligand/IonR-1,2-PROPANEDIOL
10TPN1Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
Biological Unit 2 (6, 11)
No.NameCountTypeFull Name
1APN1Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CO3-1Ligand/IonCARBONATE ION
3CPN3Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5GOL-1Ligand/IonGLYCEROL
6GPN3Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
7KPN1Mod. Amino AcidN-(2-AMINOETHYL)-N-(2,2'-BIPYRIDIN-5-YLACETYL)GLYCINE
8PGO-1Ligand/IonS-1,2-PROPANEDIOL
9PGR2Ligand/IonR-1,2-PROPANEDIOL
10TPN1Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
Biological Unit 3 (8, 12)
No.NameCountTypeFull Name
1APN1Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CO31Ligand/IonCARBONATE ION
3CPN3Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5GOL1Ligand/IonGLYCEROL
6GPN3Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
7KPN1Mod. Amino AcidN-(2-AMINOETHYL)-N-(2,2'-BIPYRIDIN-5-YLACETYL)GLYCINE
8PGO1Ligand/IonS-1,2-PROPANEDIOL
9PGR-1Ligand/IonR-1,2-PROPANEDIOL
10TPN1Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
Biological Unit 4 (8, 12)
No.NameCountTypeFull Name
1APN1Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CO31Ligand/IonCARBONATE ION
3CPN3Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5GOL1Ligand/IonGLYCEROL
6GPN3Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
7KPN1Mod. Amino AcidN-(2-AMINOETHYL)-N-(2,2'-BIPYRIDIN-5-YLACETYL)GLYCINE
8PGO1Ligand/IonS-1,2-PROPANEDIOL
9PGR-1Ligand/IonR-1,2-PROPANEDIOL
10TPN1Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGPN A:1007 , CPN A:1008 , HOH A:6108BINDING SITE FOR RESIDUE EDO A 5003
02AC2SOFTWAREGPN A:1002 , CPN A:1003 , HOH A:6021BINDING SITE FOR RESIDUE PGR A 5009
03AC3SOFTWAREGPN B:2001 , GPN B:2002 , CPN C:3009BINDING SITE FOR RESIDUE PGR B 5004
04AC4SOFTWAREGPN B:2007 , CPN B:2008BINDING SITE FOR RESIDUE PGR B 5005
05AC5SOFTWARECPN B:2009 , GPN C:3001 , GPN C:3002 , GOL C:5006 , HOH C:6038 , HOH C:6060 , HOH C:6152BINDING SITE FOR RESIDUE CO3 C 5002
06AC6SOFTWAREGPN C:3002 , CPN C:3003 , CO3 C:5002 , HOH C:6061BINDING SITE FOR RESIDUE GOL C 5006
07AC7SOFTWAREGPN C:3007 , CPN C:3008BINDING SITE FOR RESIDUE PGO C 5007
08AC8SOFTWAREGPN D:4001 , GPN D:4002 , GOL D:5010 , HOH D:6115 , HOH D:6122BINDING SITE FOR RESIDUE CO3 D 5001
09AC9SOFTWAREGPN D:4007 , CPN D:4008BINDING SITE FOR RESIDUE PGO D 5008
10BC1SOFTWAREGPN D:4002 , CPN D:4003 , CO3 D:5001BINDING SITE FOR RESIDUE GOL D 5010

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MBU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MBU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MBU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MBU)

(-) Exons   (0, 0)

(no "Exon" information available for 3MBU)

(-) 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:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                3mbu A 1001 xxxxxxxxxK 1010
                            ||||||1010
                            |||||1009-CPN
                         1001-GPN|||  
                          1002-GPN||  
                           1003-CPN|  
                            1004-APN  
                             1005-KPN 
                              1006-TPN
                               1007-GPN
                                1008-CPN


Chain B from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                3mbu B 2001 xxxxxxxxxK 2010
                            ||||||2010
                            |||||2009-CPN
                         2001-GPN|||  
                          2002-GPN||  
                           2003-CPN|  
                            2004-APN  
                             2005-KPN 
                              2006-TPN
                               2007-GPN
                                2008-CPN


Chain C from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                3mbu C 3001 xxxxxxxxxK 3010
                            ||||||3010
                            |||||3009-CPN
                         3001-GPN|||  
                          3002-GPN||  
                           3003-CPN|  
                            3004-APN  
                             3005-KPN 
                              3006-TPN
                               3007-GPN
                                3008-CPN


Chain D from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                3mbu D 4001 xxxxxxxxxK 4010
                            ||||||4010
                            |||||4009-CPN
                         4001-GPN|||  
                          4002-GPN||  
                           4003-CPN|  
                            4004-APN  
                             4005-KPN 
                              4006-TPN
                               4007-GPN
                                4008-CPN
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3MBU)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  3mbu
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3mbs