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(-) Description

Title :  ECHINOMYCIN (CGTACG)2 COMPLEX
 
Authors :  J. A. Cuesta-Seijo, G. M. Sheldrick
Date :  28 Oct 04  (Deposition) - 12 Apr 05  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,C,D,E
Keywords :  Bisintercalator, Hoogsteen Basepair, Depsipeptide, Quinoxaline, Thioacetal, Antibiotic, Antitumor, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Cuesta-Seijo, G. M. Sheldrick
Structures Of Complexes Between Echinomycin And Duplex Dna.
Acta Crystallogr. , Sect. D V. 61 442 2005
PubMed-ID: 15805599  |  Reference-DOI: 10.1107/S090744490500137X

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*TP*AP*CP*G)-3'
    Chains: A, C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - ECHINOMYCIN
    Chains: D, E
    Organism Scientific: STREPTOMYCES ECHINATUS
    Organism Taxid: 67293
    Synonym: QUINOMYCIN A

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ACDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric/Biological Unit (6, 18)
No.NameCountTypeFull Name
1DSN4Mod. Amino AcidD-SERINE
2MG2Ligand/IonMAGNESIUM ION
3MVA4Mod. Amino AcidN-METHYLVALINE
4N2C2Mod. Amino AcidN,S-DIMETHYLCYSTEINE
5NCY2Mod. Amino AcidN-METHYLCYSTEINE
6QUI4Ligand/Ion2-CARBOXYQUINOXALINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2005 , HOH A:2006 , HOH D:2001BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREHOH C:2002 , HOH C:2003 , HOH E:2001BINDING SITE FOR RESIDUE MG C 211
3AC3SOFTWAREDC A:2 , DG A:3 , DT A:4 , DG A:7 , DA C:105 , DC C:106 , DG C:107 , HOH D:2001 , HOH D:2002 , HOH D:2004 , HOH D:2005 , DSN E:5 , QUI E:9BINDING SITE FOR CHAIN D OF ECHINOMYCIN
4AC4SOFTWAREDA A:5 , DC A:6 , DG A:7 , DC C:102 , DG C:103 , DT C:104 , DG C:107 , DSN D:5 , QUI D:9 , HOH E:2001 , HOH E:2002 , HOH E:2005 , HOH E:2006 , HOH E:2007BINDING SITE FOR CHAIN E OF ECHINOMYCIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XVR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XVR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XVR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XVR)

(-) Exons   (0, 0)

(no "Exon" information available for 1XVR)

(-) 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:6
                                      
                 1xvr A   2 CGTACG   7


Chain C from PDB  Type:DNA  Length:6
                                      
                 1xvr C 102 CGTACG 107


Chain D from PDB  Type:PROTEIN  Length:8
                                        
               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
                 1xvr D   1 xAxxxAxx   8
                            | ||| ||
                            1-DSN ||
                              3-N2C|
                               4-MVA
                                5-DSN
                                  7-NCY
                                   8-MVA


Chain E from PDB  Type:PROTEIN  Length:8
                                        
               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
                 1xvr E   1 xAxxxAxx   8
                            | ||| ||
                            | ||| ||
                            1-DSN ||
                              3-N2C|
                               4-MVA
                                5-DSN
                                  7-NCY
                                   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 1XVR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XVR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XVR)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1XVR)

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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

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
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
3go3 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P41212