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Description

Title :   STRUCTURE OF ACTINOMYCIN D D(ATGCGGCAT) COMPLEX

Authors :   Y. S. Lo, W. H. Tseng, M. H. Hou

Date :   12 Oct 12 (Deposition) - 08 May 13 (Release) - 15 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Double Helix Dna, Nucleotide Flipping-Out, Sharp Kink, Left-Handed Twist, Cgg Tripleat Repeat, Neurological Disease, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. S. Lo, W. H. Tseng, C. Y. Chuang, M. H. Hou
The Structural Basis Of Actinomycin D-Binding Induces Nucleotide Flipping Out, A Sharp Bend And A Left-Handed Twist In Cgg Triplet Repeats.
Nucleic Acids Res. V. 41 4284 2013
PubMed-ID: 23408860 | Reference-DOI: 10.1093/NAR/GKT084

Compounds

*Molecule 1 - DNA (5'-D(APTPGPCPGPGPCPAPT)-3')**
	Chains	:	A, B
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - ACTINOMYCIN D
	Chains	:	C, D
	Organism Scientific	:	STREPTOMYCES ANTIBIOTICUS
	Organism Taxid	:	1890

Structural Features

Chains, Units

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 14)

Asymmetric/Biological Unit (4, 14)

No.	Name	Count	Type	Full Name
1	DVA	4	Mod. Amino Acid	D-VALINE
2	MVA	4	Mod. Amino Acid	N-METHYLVALINE
3	PXZ	2	Mod. Amino Acid	2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
4	SAR	4	Mod. Amino Acid	SARCOSINE

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DT A:2 , DG A:3 , DC A:4 , DG B:14 , DG B:15 , DC B:16 , DA B:17 , DT B:18 , SAR D:4 , MVA D:5	BINDING SITE FOR CHAIN C OF ACTINOMYCIN D
2	AC2	SOFTWARE	DC A:4 , DG A:5 , DG A:6 , DC A:7 , DA A:8 , DT B:11 , DG B:12 , DC B:13 , DVA C:2 , PRO C:9 , SAR C:10	BINDING SITE FOR CHAIN D OF ACTINOMYCIN D

SS Bonds (0, 0)

(no "SS Bond" information available for 4HIV)

Cis Peptide Bonds (6, 6)

Asymmetric/Biological Unit

No.	Residues
1	Pro C:3	-	Sar C:4
2	Pro C:9	-	Sar C:10
3	Dva D:2	-	Pro D:3
4	Pro D:3	-	Sar D:4
5	Dva D:8	-	Pro D:9
6	Pro D:9	-	Sar D:10

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 4HIV)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 4HIV)

Exons (0, 0)

(no "Exon" information available for 4HIV)

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:9
                                        
                  4hiv A  1 ATGCGGCAT  9

Chain B from PDB  Type:DNA  Length:9
                                        
                  4hiv B 10 ATGCGGCAT 18

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
                  4hiv C  1 TxPxxxTxPxx 11
                             | ||| |10|
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA

Chain D 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
                  4hiv D  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 4HIV)

CATH Domains (0, 0)

(no "CATH Domain" information available for 4HIV)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 4HIV)

Gene Ontology (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4HIV)

Visualization

Interactive Views

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		DVA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MVA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PXZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SAR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Dva D:2 - Pro D:3	[ RasMol ]
		Dva D:8 - Pro D:9	[ RasMol ]
		Pro C:3 - Sar C:4	[ RasMol ]
		Pro C:9 - Sar C:10	[ RasMol ]
		Pro D:3 - Sar D:4	[ RasMol ]
		Pro D:9 - Sar D:10	[ RasMol ]

Still Images

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	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
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	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

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