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(-) Description

Title :  CRYSTAL STRUCTURE OF 7-AMINOACTINOMYCIN D WITH NON-COMPLEMENTARY DNA
 
Authors :  E. C. Alexopoulos, R. Klement, E. A. Jares-Erijman, I. Uson, T. M. Jovin G. M. Sheldrick
Date :  11 Sep 03  (Deposition) - 24 Sep 04  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Actinomycin D, Actinomycin, Antibiotic, Anti Cancer, Chromophore, Depsipeptide, Fluorescent Agent, Anti Tumor, Non-Complementary Dna, Hoogsten Base-Pair, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. C. Alexopoulos, E. A. Jares-Erijman, T. M. Jovin, R. Klement, R. Machinek, G. M. Sheldrick, I. Uson
Crystal And Solution Structures Of 7-Amino-Actinomycin D Complexes With D(Ttagbrut), D(Ttagtt) And D(Tttagttt)
Acta Crystallogr. , Sect. D V. 61 407 2005
PubMed-ID: 15805595  |  Reference-DOI: 10.1107/S090744490500082X

(-) Compounds

Molecule 1 - 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
    Chains: A, B, C, D
    Synthetic: YES
 
Molecule 2 - 7-AMINOACTINOMYCIN D
    Chains: E, F
    Organism Scientific: STREPTOMYCES ANTIBIOTICUS
    Organism Taxid: 1890
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
1BRU4Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DVA4Mod. Amino AcidD-VALINE
3MVA4Mod. Amino AcidN-METHYLVALINE
4PX12Mod. Amino Acid(1Z)-7-AMINO-1-(HYDROXYMETHYLENE)-2-IMINO-4,6-DIMETHYL-3-OXO-2,3-DIHYDRO-1H-PHENOXAZINE-9-CARBALDEHYDE
5SAR4Mod. Amino AcidSARCOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:3 , DG A:4 , BRU A:5 , DT A:6 , DT B:6 , DG C:4 , BRU C:5 , DT D:2BINDING SITE FOR CHAIN E OF 7-AMINOACTINOMYCIN D
2AC2SOFTWAREDT A:2 , DA A:3 , HOH A:2001 , DG B:4 , BRU B:5 , DA D:3 , DG D:4 , BRU D:5 , DT D:6BINDING SITE FOR CHAIN F OF 7-AMINOACTINOMYCIN D

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Dva E:2 -Pro E:3
2Dva E:8 -Pro E:9
3Dva F:2 -Pro F:3
4Dva F:8 -Pro F:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UNM)

(-) 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
                                     
                  1unm A  1 TTAGuT  6
                                | 
                                | 
                                5-BRU


Chain B from PDB  Type:DNA  Length:5
                                    
                  1unm B  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain C from PDB  Type:DNA  Length:5
                                    
                  1unm C  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain D from PDB  Type:DNA  Length:5
                                    
                  1unm D  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain E from PDB  Type:PROTEIN  Length:11
                                          
               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
                  1unm E  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PX1|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain F from PDB  Type:PROTEIN  Length:11
                                          
               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
                  1unm F  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PX1|
                                   8-DVA
                                    10-SAR
                                     11-MVA
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 1UNM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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(-) Related Entries Specified in the PDB File

173d CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2
1a7y CRYSTAL STRUCTURE OF ACTINOMYCIN D
1a7z CRYSTAL STRUCTURE OF ACTINOMYCIN Z3
1dsc SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2
1dsd SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GATGCTTC)2
1fja SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (AAGCGCTT)2
1i3w CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CGATCGATCG)2
1l1v SOLUTION STRUCTURE OF ACTNIOMYCIN D COMPLEXED WITH MISMATCHED DNA (GTCACCGAC)
1mnv CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (ATGCTGCAT)2
1ovf SOLUTIOM STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CCGTTTTGTGG)2
1qfi CRYSTAL STRUCTURE OF ACTINOMYCIN X2
1unj CRYSTAL STRUCTURE OF 7-AMINO-ACTINOMYCIN D COMPLEXED WITH A NON-COMPLEMENTARY DNA (TTAGT)2
209d CRYSTAL STRUCTURE OF N8-ACTINOMYCIN D COMPLEXED WITH D(GAAGCTTC)2
2d55 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2
316d CRYSTAL STRUCTURE OF F8-ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2