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(-) Description

Title :  CRYSTAL STRUCUTRE OF ECHINOMYCIN-(ACGTACGT)2 SOLVED BY SAD
 
Authors :  J. A. Cuesta-Seijo, G. M. Sheldrick
Date :  21 Jul 05  (Deposition) - 28 Mar 06  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,C,E,G,H,I,J,K
Biol. Unit 1:  E,G,J,K  (1x)
Biol. Unit 2:  A,C,H,I  (1x)
Keywords :  Dna-Antibiotic Complex, Bisintercalator, Hoogsteen Basepair, Depsipeptide, Quinoxaline, Thioacetal, Antibiotic, Antitumor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Cuesta-Seijo, M. S. Weiss, G. M. Sheldrick
Serendipitous Sad Phasing Of An Echinomycin-(Acgtacgt)2 Bisintercalation Complex.
Acta Crystallogr. , Sect. D V. 62 417 2006
PubMed-ID: 16552143  |  Reference-DOI: 10.1107/S0907444906003763

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ACEGHIJK
Biological Unit 1 (1x):   EG  JK
Biological Unit 2 (1x): AC  HI  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 41)

Asymmetric Unit (8, 41)
No.NameCountTypeFull Name
1DSN8Mod. Amino AcidD-SERINE
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MVA8Mod. Amino AcidN-METHYLVALINE
4N2C7Mod. Amino AcidN,S-DIMETHYLCYSTEINE
5NCY7Mod. Amino AcidN-METHYLCYSTEINE
6NI1Ligand/IonNICKEL (II) ION
7QUI8Ligand/Ion2-CARBOXYQUINOXALINE
8ZN1Ligand/IonZINC ION
Biological Unit 1 (5, 18)
No.NameCountTypeFull Name
1DSN4Mod. Amino AcidD-SERINE
2MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MVA4Mod. Amino AcidN-METHYLVALINE
4N2C3Mod. Amino AcidN,S-DIMETHYLCYSTEINE
5NCY3Mod. Amino AcidN-METHYLCYSTEINE
6NI-1Ligand/IonNICKEL (II) ION
7QUI4Ligand/Ion2-CARBOXYQUINOXALINE
8ZN-1Ligand/IonZINC ION
Biological Unit 2 (6, 21)
No.NameCountTypeFull Name
1DSN4Mod. Amino AcidD-SERINE
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MVA4Mod. Amino AcidN-METHYLVALINE
4N2C4Mod. Amino AcidN,S-DIMETHYLCYSTEINE
5NCY4Mod. Amino AcidN-METHYLCYSTEINE
6NI-1Ligand/IonNICKEL (II) ION
7QUI4Ligand/Ion2-CARBOXYQUINOXALINE
8ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:7 , DG E:207 , HOH E:2032 , HOH E:2033 , HOH E:2034 , HOH E:2035BINDING SITE FOR RESIDUE NI E 400
2AC2SOFTWAREDG A:7 , DG E:207 , HOH E:2032 , HOH E:2033 , HOH E:2034 , HOH E:2035BINDING SITE FOR RESIDUE ZN E 401
3AC3SOFTWAREDC C:106 , DG C:107 , QUI H:9 , DSN I:1 , N2C I:3 , NCY I:7 , MVA I:8BINDING SITE FOR RESIDUE MES C 406
4AC4SOFTWAREDA A:1 , DC A:2 , DG A:3 , DT A:4 , DA C:105 , DC C:106 , DG C:107 , DT C:108 , MES C:406 , HOH H:2002 , HOH H:2004BINDING SITE FOR LINKED RESIDUES H 0 to 9
5AC5SOFTWAREDA A:5 , DC A:6 , DG A:7 , DT A:8 , HOH A:2015 , DA C:101 , DC C:102 , DG C:103 , DT C:104 , MES C:406 , DA E:201 , DT G:308 , HOH G:2007 , HOH I:2001 , HOH I:2002 , DSN K:1 , N2C K:3 , NCY K:7 , MVA K:8BINDING SITE FOR LINKED RESIDUES I 0 to 9
6AC6SOFTWAREDT A:8 , DA C:101 , DA E:205 , DC E:206 , DG E:207 , DT E:208 , HOH E:2034 , DA G:301 , DC G:302 , DG G:303 , DT G:304 , HOH J:2001 , HOH J:2002 , HOH J:2003 , HOH J:2004BINDING SITE FOR LINKED RESIDUES J 0 to 9
7AC7SOFTWAREDC A:6 , DA E:201 , DC E:202 , DG E:203 , DT E:204 , DA G:305 , DC G:306 , DG G:307 , DT G:308 , N2C I:3 , MVA I:4 , HOH K:2001 , HOH K:2002 , HOH K:2005 , HOH K:2006BINDING SITE FOR LINKED RESIDUES K 0 to 9

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ADW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ADW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ADW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ADW)

(-) Exons   (0, 0)

(no "Exon" information available for 2ADW)

(-) 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:DNA  Length:8
                                        
                 2adw A   1 ACGTACGT   8


Chain C from PDB  Type:DNA  Length:8
                                        
                 2adw C 101 ACGTACGT 108


Chain E from PDB  Type:DNA  Length:8
                                        
                 2adw E 201 ACGTACGT 208


Chain G from PDB  Type:DNA  Length:8
                                        
                 2adw G 301 ACGTACGT 308


Chain H 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
                 2adw H   1 xAxxxxAxxx   8
                            | |||| ||8
                            1-DSN| |||
                              3-N2C|||
                               3-NCY||
                                4-MVA|
                                 5-DSN
                                   7-NCY
                                    7-N2C
                                     8-MVA


Chain I 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
                 2adw I   1 xAxxxxAxxx   8
                            | |||| ||8
                            | |||| |||
                            1-DSN| |||
                              3-N2C|||
                               3-NCY||
                                4-MVA|
                                 5-DSN
                                   7-NCY
                                    7-N2C
                                     8-MVA


Chain J 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
                 2adw J   1 xAxxxxAxxx   8
                            | |||| ||8
                            | |||| |||
                            1-DSN| |||
                              3-N2C|||
                               3-NCY||
                                4-MVA|
                                 5-DSN
                                   7-NCY
                                    7-N2C
                                     8-MVA


Chain K 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
                 2adw K   1 xAxxxAxx   8
                            | ||| ||
                            | ||| ||
                            1-DSN ||
                              3-N2C|
                               4-MVA
                                5-DSN
                                  7-NCY
                                   8-MVA
   Legend:   → Mismatch (orange background)
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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 2ADW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ADW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ADW)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2ADW)

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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
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