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(-) Description

Title :  ACTINOMYCIN D BINDING TO CGATCGATCG
 
Authors :  H. Robinson, Y. -G. Gao, X. -L. Yang, R. Sanishvili, A. Joachimiak, A. H.
Date :  17 Feb 01  (Deposition) - 21 May 01  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Actinomycin D, Actinomycin, Antibiotic, Anti Cancer, Antitumor, Mismatch, Chromophore, Depsipeptide, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Robinson, Y. G. Gao, X. Yang, R. Sanishvili, A. Joachimiak, A. H. Wan
Crystallographic Analysis Of A Novel Complex Of Actinomycin D Bound To The Dna Decamer Cgatcgatcg.
Biochemistry V. 40 5587 2001
PubMed-ID: 11341823  |  Reference-DOI: 10.1021/BI002859Z

(-) Compounds

Molecule 1 - 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
    Chains: A, B, C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - ACTINOMYCIN D
    Chains: E, F, G, H
    Organism Scientific: STREPTOMYCES ANTIBIOTICUS
    Organism Taxid: 1890
    Synonym: DACTINOMYCIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 32)

Asymmetric Unit (5, 32)
No.NameCountTypeFull Name
1BRU4Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DVA8Mod. Amino AcidD-VALINE
3MVA8Mod. Amino AcidN-METHYLVALINE
4PXZ4Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
5SAR8Mod. Amino AcidSARCOSINE
Biological Unit 1 (5, 16)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DVA4Mod. Amino AcidD-VALINE
3MVA4Mod. Amino AcidN-METHYLVALINE
4PXZ2Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
5SAR4Mod. Amino AcidSARCOSINE
Biological Unit 2 (5, 16)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DVA4Mod. Amino AcidD-VALINE
3MVA4Mod. Amino AcidN-METHYLVALINE
4PXZ2Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
5SAR4Mod. Amino AcidSARCOSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:2 , DA A:3 , DC A:5 , DG A:6 , DC B:11 , DC B:19 , DG B:20 , DT C:24 , HOH E:2005 , HOH E:2006 , HOH E:2008 , HOH E:2009BINDING SITE FOR CHAIN E OF ACTINOMYCIN D
2AC2SOFTWAREDG A:2 , DC A:9 , DG A:10 , DC B:11 , DG B:12 , DA B:13 , DC B:15 , DG B:16 , DT D:34 , HOH F:2004 , HOH F:2006 , HOH F:2007 , HOH F:2008 , HOH F:2009 , MVA H:11BINDING SITE FOR CHAIN F OF ACTINOMYCIN D
3AC3SOFTWAREDT A:4 , DG C:22 , DA C:23 , DC C:25 , DG C:26 , DC D:31 , DG D:40 , HOH G:2007 , HOH G:2008 , HOH G:2010BINDING SITE FOR CHAIN G OF ACTINOMYCIN D
4AC4SOFTWAREDT B:14 , DG C:22 , DG C:30 , DC D:31 , DG D:32 , DA D:33 , DC D:35 , DG D:36 , MVA F:11 , HOH H:2001 , HOH H:2003 , HOH H:2004 , HOH H:2005 , HOH H:2006 , HOH H:2007BINDING SITE FOR CHAIN H OF ACTINOMYCIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I3W)

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Dva E:2 -Pro E:3
2Pro E:3 -Sar E:4
3Pro E:9 -Sar E:10
4Dva F:2 -Pro F:3
5Pro F:3 -Sar F:4
6Dva F:8 -Pro F:9
7Pro F:9 -Sar F:10
8Pro G:3 -Sar G:4
9Dva G:8 -Pro G:9
10Pro G:9 -Sar G:10
11Dva H:2 -Pro H:3
12Pro H:3 -Sar H:4
13Dva H:8 -Pro H:9
14Pro H:9 -Sar H:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I3W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I3W)

(-) Exons   (0, 0)

(no "Exon" information available for 1I3W)

(-) 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:9
                                        
                  1i3w A  2 GATCGAuCG 10
                                  |  
                                  8-BRU


Chain B from PDB  Type:DNA  Length:10
                                         
                  1i3w B 11 CGATCGAuCG 20
                                   |20
                                  18-BRU


Chain C from PDB  Type:DNA  Length:9
                                        
                  1i3w C 22 GATCGAuCG 30
                                  |  
                                 28-BRU


Chain D from PDB  Type:DNA  Length:10
                                         
                  1i3w D 31 CGATCGAuCG 40
                                   |40
                                  38-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
                  1i3w E  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   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
                  1i3w F  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain G 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
                  1i3w G  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain H 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
                  1i3w H  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 1I3W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1I3W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I3W)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1I3W)

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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
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
1unm CRYSTAL STRUCTURE OF 7-AMINOACTINOMYCIN D COMPLEXED WITH NON-COMPLEMENTARY DNA
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