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(-) Description

Title :  CRYSTAL STRUCTURE OF A 7-AMINOACTINOMYCIN D COMPLEX WITH NON-COMPLEMENTARY DNA
 
Authors :  E. C. Alexopoulos, R. Klement, E. A. Jares-Erijman, I. Uson, T. M. Jovin G. M. Sheldrick
Date :  10 Sep 03  (Deposition) - 16 Dec 04  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Biol. Unit 1:  A,B,C,D,E,F,G,H,I,J,K,L  (1x)
Biol. Unit 2:  M,N,O,P,Q,R,S,T,U,V,W,X  (1x)
Keywords :  Actinomycin D, Actinomycin, Antibiotic, Anti Cancer, Antitumor, Chromophore, Depsipeptide, Dna-Antibiotic Complex, Fluorescent Agent, Hoogsten Base-Pair (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, G, H, I, J, M, N, O, P, S, T, U, V
    Synthetic: YES
 
Molecule 2 - 7-AMINO-ACTINOMYCIN D
    Chains: E, F, K, L, Q, R, W, X
    Organism Scientific: STREPTOMYCES ANTIBIOTICUS
    Organism Taxid: 1890
    Synonym: DACTINOMYCIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112131415161718192021222324
Asymmetric Unit : ABCDEFGHIJKLMNOPQRSTUVWX
Biological Unit 1 (1x): ABCDEFGHIJKL            
Biological Unit 2 (1x):             MNOPQRSTUVWX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 72)

Asymmetric Unit (5, 72)
No.NameCountTypeFull Name
1BRU16Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DVA16Mod. Amino AcidD-VALINE
3MVA16Mod. Amino AcidN-METHYLVALINE
4PX18Mod. Amino Acid(1Z)-7-AMINO-1-(HYDROXYMETHYLENE)-2-IMINO-4,6-DIMETHYL-3-OXO-2,3-DIHYDRO-1H-PHENOXAZINE-9-CARBALDEHYDE
5SAR16Mod. Amino AcidSARCOSINE
Biological Unit 1 (5, 36)
No.NameCountTypeFull Name
1BRU8Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DVA8Mod. Amino AcidD-VALINE
3MVA8Mod. Amino AcidN-METHYLVALINE
4PX14Mod. Amino Acid(1Z)-7-AMINO-1-(HYDROXYMETHYLENE)-2-IMINO-4,6-DIMETHYL-3-OXO-2,3-DIHYDRO-1H-PHENOXAZINE-9-CARBALDEHYDE
5SAR8Mod. Amino AcidSARCOSINE
Biological Unit 2 (5, 36)
No.NameCountTypeFull Name
1BRU8Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DVA8Mod. Amino AcidD-VALINE
3MVA8Mod. Amino AcidN-METHYLVALINE
4PX14Mod. Amino Acid(1Z)-7-AMINO-1-(HYDROXYMETHYLENE)-2-IMINO-4,6-DIMETHYL-3-OXO-2,3-DIHYDRO-1H-PHENOXAZINE-9-CARBALDEHYDE
5SAR8Mod. Amino AcidSARCOSINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:3 , DG A:4 , BRU A:5 , DT A:6 , DA C:3 , DG C:4 , BRU C:5 , DT H:6 , DT J:2 , BRU T:5 , DT V:1BINDING SITE FOR CHAIN E OF 7-AMINO-ACTINOMYCIN D
2AC2SOFTWAREDG B:4 , BRU B:5 , DA D:3 , DG D:4 , BRU D:5 , DT D:6 , DT G:2 , DA G:3BINDING SITE FOR CHAIN F OF 7-AMINO-ACTINOMYCIN D
3AC3SOFTWAREDT B:6 , DT D:2 , DA G:3 , DG G:4 , BRU G:5 , DT G:6 , DA I:3 , DG I:4 , BRU I:5 , DVA L:2BINDING SITE FOR CHAIN K OF 7-AMINO-ACTINOMYCIN D
4AC4SOFTWAREDT A:2 , DA A:3 , DG H:4 , BRU H:5 , DA J:3 , DG J:4 , BRU J:5 , DT J:6 , DVA K:8BINDING SITE FOR CHAIN L OF 7-AMINO-ACTINOMYCIN D
5AC5SOFTWAREDA M:3 , DG M:4 , BRU M:5 , DT M:6 , DG O:4 , BRU O:5 , HOH Q:2001 , DVA R:2 , SAR R:4 , DVA R:8 , DT T:6 , DT V:2BINDING SITE FOR CHAIN Q OF 7-AMINO-ACTINOMYCIN D
6AC6SOFTWAREDA N:3 , DG N:4 , BRU N:5 , DA P:3 , DG P:4 , BRU P:5 , DT P:6 , DVA Q:2 , DVA Q:8 , DT S:2 , DA S:3BINDING SITE FOR CHAIN R OF 7-AMINO-ACTINOMYCIN D
7AC7SOFTWAREDT N:6 , DT P:2 , DA S:3 , DG S:4 , BRU S:5 , DT S:6 , DG U:4 , BRU U:5 , HOH W:2001 , DVA X:2BINDING SITE FOR CHAIN W OF 7-AMINO-ACTINOMYCIN D
8AC8SOFTWAREDT M:2 , DA M:3 , DT S:6 , DA T:3 , DG T:4 , BRU T:5 , DA V:3 , DG V:4 , BRU V:5 , DT V:6 , DVA W:2 , DVA W:8BINDING SITE FOR CHAIN X OF 7-AMINO-ACTINOMYCIN D

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (16, 16)

Asymmetric 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
5Dva K:2 -Pro K:3
6Dva K:8 -Pro K:9
7Dva L:2 -Pro L:3
8Dva L:8 -Pro L:9
9Dva Q:2 -Pro Q:3
10Dva Q:8 -Pro Q:9
11Dva R:2 -Pro R:3
12Dva R:8 -Pro R:9
13Dva W:2 -Pro W:3
14Dva W:8 -Pro W:9
15Dva X:2 -Pro X:3
16Dva X:8 -Pro X:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UNJ)

(-) 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:5
                                    
                  1unj A  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain B from PDB  Type:DNA  Length:4
                                   
                  1unj B  3 AGuT  6
                              | 
                              | 
                              5-BRU


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


Chain D from PDB  Type:DNA  Length:5
                                    
                  1unj 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
                  1unj 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
                  1unj F  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PX1|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain G from PDB  Type:DNA  Length:5
                                    
                  1unj G  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain H from PDB  Type:DNA  Length:4
                                   
                  1unj H  3 AGuT  6
                              | 
                              | 
                              5-BRU


Chain I from PDB  Type:DNA  Length:5
                                    
                  1unj I  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain J from PDB  Type:DNA  Length:5
                                    
                  1unj J  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain K 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
                  1unj K  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PX1|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain L 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
                  1unj L  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PX1|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain M from PDB  Type:DNA  Length:5
                                    
                  1unj M  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain N from PDB  Type:DNA  Length:5
                                    
                  1unj N  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain O from PDB  Type:DNA  Length:5
                                    
                  1unj O  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain P from PDB  Type:DNA  Length:5
                                    
                  1unj P  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain Q 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
                  1unj Q  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PX1|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain R 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
                  1unj R  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PX1|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain S from PDB  Type:DNA  Length:5
                                    
                  1unj S  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain T from PDB  Type:DNA  Length:5
                                    
                  1unj T  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain U from PDB  Type:DNA  Length:5
                                    
                  1unj U  2 TAGuT  6
                               | 
                               | 
                               5-BRU


Chain V from PDB  Type:DNA  Length:6
                                     
                  1unj V  1 TTAGuT  6
                                | 
                                5-BRU


Chain W 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
                  1unj W  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PX1|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain X 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
                  1unj X  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 1UNJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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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
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