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(-) Description

Title :  INFLUENCE OF THE INCORPORATION OF A CYCLOHEXENYL NUCLEIC ACID (CENA) RESIDUE ONTO THE SEQUENCE D(GCGTGCG)/D(CGCACGC)
 
Authors :  K. Robeyns, P. Herdewijn, L. Van Meervelt
Date :  18 Dec 08  (Deposition) - 29 Dec 09  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.17
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Double Helix, Cena, Sugar Modification, Right-Handed, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Robeyns, P. Herdewijn, L. Van Meervelt
Direct Observation Of Two Cyclohexenyl (Cena) Ring Conformations In Duplex Dna.
Artif Dna Pna Xna V. 1 2 2010
PubMed-ID: 21687521  |  Reference-DOI: 10.4161/ADNA.1.1.10952
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3'
    Chains: A, C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
    Chains: B, 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, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1NCO7Ligand/IonCOBALT HEXAMMINE(III)
2XTR2Mod. Nucleotide[(1R,4S,6S)-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYLDIHYDROGEN PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NCO3Ligand/IonCOBALT HEXAMMINE(III)
2XTR1Mod. Nucleotide[(1R,4S,6S)-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYLDIHYDROGEN PHOSPHATE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1NCO4Ligand/IonCOBALT HEXAMMINE(III)
2XTR1Mod. Nucleotide[(1R,4S,6S)-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYLDIHYDROGEN PHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREXTR A:4 , DG A:7 , HOH A:165 , HOH A:175 , HOH A:211 , DC B:1 , HOH B:144 , DG C:3 , HOH C:233BINDING SITE FOR RESIDUE NCO A 63
2AC2SOFTWAREDC B:1 , DC B:3 , DA B:4 , HOH B:106 , DG C:1 , HOH C:166 , HOH C:186 , HOH C:214 , DG D:6 , DC D:7BINDING SITE FOR RESIDUE NCO B 61
3AC3SOFTWAREDC B:5 , DG C:3 , HOH C:225 , DC D:1 , DC D:5BINDING SITE FOR RESIDUE NCO B 65
4AC4SOFTWAREHOH A:101 , XTR C:4 , DG C:5 , DG C:7 , HOH C:139BINDING SITE FOR RESIDUE NCO C 64
5AC5SOFTWAREDC A:2 , DG A:3 , HOH A:167 , HOH A:210 , HOH C:179 , HOH C:189 , DC D:1BINDING SITE FOR RESIDUE NCO C 66
6AC6SOFTWAREDC A:6 , DG A:7 , HOH A:135 , HOH A:226 , DC C:2 , DC D:7BINDING SITE FOR RESIDUE NCO C 67
7AC7SOFTWAREDG A:1 , DC A:2 , DG B:6 , DC B:7 , DG D:2BINDING SITE FOR RESIDUE NCO D 62

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FL6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FL6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FL6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FL6)

(-) Exons   (0, 0)

(no "Exon" information available for 3FL6)

(-) 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  Length:7
                                     
                   3fl6 A 1 GCGtGCG 7
                               |   
                               |   
                               4-XTR


Chain B from PDB  Type:DNA  Length:7
                                     
                   3fl6 B 1 CGCACGC 7


Chain C from PDB  Type:DNA  Length:7
                                     
                   3fl6 C 1 GCGtGCG 7
                               |   
                               4-XTR


Chain D from PDB  Type:DNA  Length:7
                                     
                   3fl6 D 1 CGCACGC 7
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3FL6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FL6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FL6)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

2h0n CONTAINS THE SAME TYPE OF SYNTHETIC NUCLEOSIDES
2p8d CONTAINS THE SAME TYPE OF SYNTHETIC NUCLEOSIDES