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(-) Description

Title :  A CONFORMATIONAL TRANSITION IN THE STRUCTURE OF A 2'-THIOMETHYL-MODIFIED DNA VISUALIZED AT HIGH RESOLUTION
 
Authors :  M. Egli, P. S. Pallan
Date :  17 Oct 08  (Deposition) - 28 Apr 09  (Release) - 26 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B,C,D,E#
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Modified Dna Duplex, Crystal Structure, 2'-Thiomethyl Uridine, Modified Sugar (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. S. Pallan, T. P. Prakash, F. Li, R. L. Eoff, M. Manoharan, M. Egli
A Conformational Transition In The Structure Of A 2'-Thiomethyl-Modified Dna Visualized At High Resolution.
Chem. Commun. (Camb. ) 2017 2009
PubMed-ID: 19333476  |  Reference-DOI: 10.1039/B822781K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM) P*CP*GP*CP*G)-3'
    ChainsA, B, C, D
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED MODIFIED DNA (OLIGONUCLEOTIDE)
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE#
Biological Unit 1 (1x)AB   
Biological Unit 2 (1x)  CD 
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SR7Ligand/IonSTRONTIUM ION
3USM8Mod. Nucleotide2'-S-METHYL-2'-THIOURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SR-1Ligand/IonSTRONTIUM ION
3USM4Mod. Nucleotide2'-S-METHYL-2'-THIOURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SR-1Ligand/IonSTRONTIUM ION
3USM4Mod. Nucleotide2'-S-METHYL-2'-THIOURIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA B:205 , HOH B:601 , HOH B:602 , HOH B:603 , HOH B:604 , HOH B:629 , HOH B:872 , HOH B:879BINDING SITE FOR RESIDUE SR B 501
2AC2SOFTWAREDG D:412 , HOH D:721 , HOH D:722 , HOH D:723 , HOH D:724 , HOH D:725 , HOH D:726 , HOH D:873BINDING SITE FOR RESIDUE SR D 502
3AC3SOFTWAREHOH C:605 , HOH C:606 , HOH C:609 , HOH C:665 , HOH C:728 , HOH D:607 , HOH D:608 , HOH D:727BINDING SITE FOR RESIDUE SR C 503
4AC4SOFTWAREHOH A:612 , HOH A:615 , HOH A:616 , HOH A:617 , HOH B:610 , HOH B:611 , HOH B:613 , HOH B:614BINDING SITE FOR RESIDUE SR A 504
5AC5SOFTWAREHOH C:618 , HOH C:620 , HOH C:729 , HOH C:730 , HOH C:871 , HOH C:938 , HOH D:619 , HOH D:666BINDING SITE FOR RESIDUE SR D 505
6AC6SOFTWAREHOH A:623 , HOH A:710 , HOH A:719 , HOH A:870 , HOH A:877 , HOH A:930 , HOH A:931 , HOH B:878BINDING SITE FOR RESIDUE SR A 506
7AC7SOFTWAREHOH C:642 , HOH C:720 , HOH C:805 , HOH C:874 , HOH C:875 , HOH C:876 , HOH C:929BINDING SITE FOR RESIDUE SR C 507
8AC8SOFTWAREDG B:212 , HOH B:764 , HOH C:677 , DA D:406 , USM D:407 , HOH D:634 , HOH D:708BINDING SITE FOR RESIDUE MPD D 1001
9AC9SOFTWAREHOH A:633 , DA B:206 , USM B:207 , HOH B:643BINDING SITE FOR RESIDUE MPD B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EY3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EY3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EY3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EY3)

(-) Exons   (0, 0)

(no "Exon" information available for 3EY3)

(-) 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
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Chain A from PDB  Type:DNA  Length:12
                                            
                 3ey3 A 101 CGCGAAxxCGCG 112
                                  |110  
                                  ||    
                                107-USM 
                                 108-USM

Chain B from PDB  Type:DNA  Length:12
                                            
                 3ey3 B 201 CGCGAAxxCGCG 212
                                  |210  
                                207-USM 
                                 208-USM

Chain C from PDB  Type:DNA  Length:12
                                            
                 3ey3 C 301 CGCGAAxxCGCG 312
                                  |310  
                                307-USM 
                                 308-USM

Chain D from PDB  Type:DNA  Length:12
                                            
                 3ey3 D 401 CGCGAAxxCGCG 412
                                  |410  
                                407-USM 
                                 408-USM

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 3EY3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EY3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EY3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3EY3)

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3EY3)

(-) Related Entries Specified in the PDB File

3ey1 3ey2