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(-) Description

Title :  INTERACTIONS OF AN ECHINOMYCIN-DNA COMPLEX WITH MANGANESE(II) IONS
 
Authors :  R. Pfoh, J. A. Cuesta-Seijo, G. M. Sheldrick
Date :  18 Mar 09  (Deposition) - 31 Mar 09  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Bisintercalator, Hoogsteen Basepair, Depsipeptide, Quinoxaline, Thioacetal, Antibiotic, Antitumor, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Pfoh, J. A. Cuesta-Seijo, G. M. Sheldrick
Interaction Of An Echinomycin-Dna Complex With Manganese Io
Acta Crystallogr. , Sect. F V. 65 660 2009
PubMed-ID: 19574634  |  Reference-DOI: 10.1107/S1744309109019654

(-) Compounds

Molecule 1 - 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
    Chains: A, B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - ECHINOMYCIN
    Chains: C, D
    Organism Scientific: STREPTOMYCES ECHINATUS
    Organism Taxid: 67293
    Synonym: QUINOMYCIN A

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 23)

Asymmetric/Biological Unit (7, 23)
No.NameCountTypeFull Name
1DSN4Mod. Amino AcidD-SERINE
2MN2Ligand/IonMANGANESE (II) ION
3MVA4Mod. Amino AcidN-METHYLVALINE
4N2C4Mod. Amino AcidN,S-DIMETHYLCYSTEINE
5NCY4Mod. Amino AcidN-METHYLCYSTEINE
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7QUI4Ligand/Ion2-CARBOXYQUINOXALINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:1 , DG B:103 , DT B:104BINDING SITE FOR RESIDUE PEG B 301
2AC2SOFTWAREDG A:3 , HOH A:2029 , HOH A:2030BINDING SITE FOR RESIDUE MN A 401
3AC3SOFTWAREDC A:6 , DG B:107 , HOH B:2011 , HOH B:2012 , HOH B:2013 , HOH B:2014BINDING SITE FOR RESIDUE MN B 401
4AC4SOFTWAREDA A:1 , DC A:2 , DG A:3 , DT A:4 , DT A:8 , HOH A:2030 , DA B:105 , DC B:106 , DG B:107 , DT B:108 , HOH B:2014 , HOH C:2001BINDING SITE FOR LINKED RESIDUES C 0 to 9
5AC5SOFTWAREDA A:5 , DC A:6 , DG A:7 , DT A:8 , HOH A:2006 , DA B:101 , DC B:102 , DG B:103 , DT B:104BINDING SITE FOR LINKED RESIDUES D 0 to 9

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GO3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GO3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GO3)

(-) Exons   (0, 0)

(no "Exon" information available for 3GO3)

(-) Sequences/Alignments

Asymmetric/Biological 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:DNA  Length:8
                                        
                 3go3 A   1 ACGTACGT   8


Chain B from PDB  Type:DNA  Length:8
                                        
                 3go3 B 101 ACGTACGT 108


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
                 3go3 C   1 xAxxxxAxxx   8
                            | |||| ||8
                            1-DSN| |||
                              3-N2C|||
                               3-NCY||
                                4-MVA|
                                 5-DSN
                                   7-NCY
                                    7-N2C
                                     8-MVA


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
                 3go3 D   1 xAxxxxAxxx   8
                            | |||| ||8
                            | |||| |||
                            1-DSN| |||
                              3-N2C|||
                               3-NCY||
                                4-MVA|
                                 5-DSN
                                   7-NCY
                                    7-N2C
                                     8-MVA
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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 3GO3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GO3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GO3)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

185d SOLUTION STRUCTURE OF D(GACGTC) COMPLEXED WITH TRIOSTIN A
193d SOLUTION STRUCTURE OF D(ACACGTGT) COMPLEXED WITH QUINOMYCIN UK-6305
1pfe CRYSTAL STRUCTURE OF D(GCGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P6322
1vs2 CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A
1xvk CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632
1xvn CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632
1xvr CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP C21
2adw CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P42212
2da8 SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN A AT POSITIONS 4 AND 8