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(-) Description

Title :  CRYSTAL STRUCTURE OF ACTINOMYCIN D
 
Authors :  M. Schafer, G. M. Sheldrick, I. Bahner, H. Lackner
Date :  19 Mar 98  (Deposition) - 23 Mar 99  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.94
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Actinomycin, Antibiotic, Antitumor, Anticancer, Chromophore, Depsipeptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schaefer, G. M. Sheldrick, I. Bahner, H. Lackner
Crystal Structures Of Actinomycin D And Actinomycin Z3
Angew. Chem. Int. Ed. Engl. V. 37 2381 1998

(-) Compounds

Molecule 1 - ACTINOMYCIN D
    Chains: A, B, C
    Organism Scientific: STREPTOMYCES ANTIBIOTICUS
    Organism Taxid: 1890
    Synonym: DACTINOMYCIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 29)

Asymmetric Unit (6, 29)
No.NameCountTypeFull Name
1DVA6Mod. Amino AcidD-VALINE
2EEE7Ligand/IonETHYL ACETATE
3MOH1Ligand/IonMETHANOL
4MVA6Mod. Amino AcidN-METHYLVALINE
5PXZ3Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
6SAR6Mod. Amino AcidSARCOSINE
Biological Unit 1 (5, 11)
No.NameCountTypeFull Name
1DVA2Mod. Amino AcidD-VALINE
2EEE4Ligand/IonETHYL ACETATE
3MOH-1Ligand/IonMETHANOL
4MVA2Mod. Amino AcidN-METHYLVALINE
5PXZ1Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
6SAR2Mod. Amino AcidSARCOSINE
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1DVA2Mod. Amino AcidD-VALINE
2EEE-1Ligand/IonETHYL ACETATE
3MOH-1Ligand/IonMETHANOL
4MVA2Mod. Amino AcidN-METHYLVALINE
5PXZ1Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
6SAR2Mod. Amino AcidSARCOSINE
Biological Unit 3 (6, 11)
No.NameCountTypeFull Name
1DVA2Mod. Amino AcidD-VALINE
2EEE3Ligand/IonETHYL ACETATE
3MOH1Ligand/IonMETHANOL
4MVA2Mod. Amino AcidN-METHYLVALINE
5PXZ1Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
6SAR2Mod. Amino AcidSARCOSINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDVA A:8 , EEE A:105 , PRO C:3 , PXZ C:6 , EEE C:101BINDING SITE FOR RESIDUE EEE A 104
02AC2SOFTWARETHR A:1 , THR A:7 , EEE A:104 , SAR B:10BINDING SITE FOR RESIDUE EEE A 105
03AC3SOFTWAREMVA A:5 , THR A:7 , PXZ C:6BINDING SITE FOR RESIDUE EEE A 106
04AC4SOFTWAREPRO A:3 , DVA B:2 , PRO B:3 , THR C:1 , PXZ C:6 , PRO C:9BINDING SITE FOR RESIDUE EEE A 107
05AC5SOFTWAREEEE A:104 , MVA C:5BINDING SITE FOR RESIDUE EEE C 101
06AC6SOFTWARESAR A:10 , THR B:1 , MVA B:5 , PXZ B:6 , PRO C:3 , EEE C:103BINDING SITE FOR RESIDUE EEE C 102
07AC7SOFTWAREMVA B:5 , PXZ B:6 , DVA B:8 , PRO C:9 , MVA C:11 , EEE C:102BINDING SITE FOR RESIDUE EEE C 103
08AC8SOFTWAREEEE A:104 , EEE A:105 , EEE A:106 , EEE A:107 , THR B:1 , PXZ B:6 , THR B:7 , PRO B:9 , MVA B:11 , PRO C:3 , SAR C:4 , MVA C:5 , PXZ C:6 , EEE C:102BINDING SITE FOR CHAIN A OF ACTINOMYCIN D
09AC9SOFTWARETHR A:1 , PXZ A:6 , THR A:7 , PRO A:9 , MVA A:11 , EEE A:105 , EEE A:107 , DVA C:2 , PXZ C:6 , DVA C:8 , PRO C:9 , SAR C:10 , MVA C:11 , EEE C:102 , EEE C:103BINDING SITE FOR CHAIN B OF ACTINOMYCIN D
10BC1SOFTWAREDVA A:2 , PRO A:3 , SAR A:4 , MVA A:5 , PXZ A:6 , EEE A:104 , EEE A:106 , EEE A:107 , PRO B:3 , MVA B:5 , PXZ B:6 , DVA B:8 , MVA B:11 , EEE C:101 , EEE C:102 , EEE C:103BINDING SITE FOR CHAIN C OF ACTINOMYCIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A7Y)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Dva A:2 -Pro A:3
2Pro A:3 -Sar A:4
3Dva A:8 -Pro A:9
4Pro A:9 -Sar A:10
5Dva B:2 -Pro B:3
6Pro B:3 -Sar B:4
7Dva B:8 -Pro B:9
8Pro B:9 -Sar B:10
9Dva C:2 -Pro C:3
10Pro C:3 -Sar C:4
11Dva C:8 -Pro C:9
12Pro C:9 -Sar C:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1A7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1A7Y)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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: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
                  1a7y A  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain B 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
                  1a7y B  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain C 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
                  1a7y C  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-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 1A7Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1A7Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A7Y)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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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
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
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