1VAQ | DD0063 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE MG2+-(CHROMOMYCIN A3)2-D(TTGGCCAA) 2 COMPLEX REVEALS GGCC BINDING SPECIFICITY OF THE DRUG DIMER CHELATED BY METAL ION

Authors :   M. H. Hou, H. Robinson, Y. G. Gao, A. H. -J. Wang

Date :   19 Feb 04 (Deposition) - 22 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Chromomycin A3, X-Ray Diffraction, Mad, Dna Duplex, Ggcc Site, Dna Kink, Cd Spectra (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. H. Hou, H. Robinson, Y. G. Gao, A. H. -J. Wang
Crystal Structure Of The [Mg2+-(Chromomycin A3)2]-D(Ttggccaa)2 Complex Reveals Ggcc Binding Specificity Of The Drug Dimer Chelated By A Metal Ion
Nucleic Acids Res. V. 32 2214 2004
PubMed-ID: 15107489 | Reference-DOI: 10.1093/NAR/GKH549
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 26)

Asymmetric Unit (6, 26)

No.	Name	Count	Type	Full Name
1	1GL	4	Ligand/Ion	4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
2	ARI	4	Ligand/Ion	[O4]-ACETOXY-2,3-DIDEOXYFUCOSE
3	CDR	8	Ligand/Ion	2,3-DIDEOXYFUCOSE
4	CPH	4	Ligand/Ion	1,8-DIHYDROXY-7-METHYL-3-(1,3,4-TRIHYDROXY-2-OXO-PENTYL)-3,10-DIHYDRO-2H-ANTHRACEN-9-ONE
5	ERI	4	Ligand/Ion	4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE
6	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (5, 12)

No.	Name	Count	Type	Full Name
1	1GL	2	Ligand/Ion	4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
2	ARI	2	Ligand/Ion	[O4]-ACETOXY-2,3-DIDEOXYFUCOSE
3	CDR	4	Ligand/Ion	2,3-DIDEOXYFUCOSE
4	CPH	2	Ligand/Ion	1,8-DIHYDROXY-7-METHYL-3-(1,3,4-TRIHYDROXY-2-OXO-PENTYL)-3,10-DIHYDRO-2H-ANTHRACEN-9-ONE
5	ERI	2	Ligand/Ion	4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE
6	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (5, 12)

No.	Name	Count	Type	Full Name
1	1GL	2	Ligand/Ion	4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
2	ARI	2	Ligand/Ion	[O4]-ACETOXY-2,3-DIDEOXYFUCOSE
3	CDR	4	Ligand/Ion	2,3-DIDEOXYFUCOSE
4	CPH	2	Ligand/Ion	1,8-DIHYDROXY-7-METHYL-3-(1,3,4-TRIHYDROXY-2-OXO-PENTYL)-3,10-DIHYDRO-2H-ANTHRACEN-9-ONE
5	ERI	2	Ligand/Ion	4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE
6	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (26, 26)

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	DG B:12 , DC B:13 , ARI B:22 , DA C:48 , HOH C:358	BINDING SITE FOR RESIDUE 1GL B 21
02	AC2	SOFTWARE	1GL B:21 , CPH B:23 , CDR B:35 , ERI B:36	BINDING SITE FOR RESIDUE ARI B 22
03	AC3	SOFTWARE	DC B:14 , CPH B:23 , CDR B:25 , HOH B:404 , CPH C:73	BINDING SITE FOR RESIDUE CDR B 24
04	AC4	SOFTWARE	ARI A:32 , CPH A:33 , DA B:15 , CDR B:24 , ERI B:26 , CPH C:73	BINDING SITE FOR RESIDUE CDR B 25
05	AC5	SOFTWARE	DG A:3 , DG A:4 , ARI A:32 , CPH A:33 , DA B:15 , CDR B:25 , HOH B:236	BINDING SITE FOR RESIDUE ERI B 26
06	AC6	SOFTWARE	DG A:4 , ARI A:32 , HOH A:417	BINDING SITE FOR RESIDUE 1GL A 31
07	AC7	SOFTWARE	DC A:5 , 1GL A:31 , CPH A:33 , HOH A:240 , CDR B:25 , ERI B:26	BINDING SITE FOR RESIDUE ARI A 32
08	AC8	SOFTWARE	DC A:6 , CPH A:33 , CDR B:35 , HOH B:359 , HOH B:467 , CDR C:74 , CPH D:63	BINDING SITE FOR RESIDUE CDR B 34
09	AC9	SOFTWARE	ARI B:22 , CPH B:23 , CDR B:34 , ERI B:36 , ARI D:62	BINDING SITE FOR RESIDUE CDR B 35
10	BC1	SOFTWARE	DA A:7 , DG B:11 , ARI B:22 , CPH B:23 , CDR B:35 , HOH B:383 , HOH B:384	BINDING SITE FOR RESIDUE ERI B 36
11	BC2	SOFTWARE	DG D:52 , DC D:53 , ARI D:62 , HOH D:323	BINDING SITE FOR RESIDUE 1GL D 61
12	BC3	SOFTWARE	CDR B:35 , CDR C:75 , ERI C:76 , 1GL D:61 , CPH D:63	BINDING SITE FOR RESIDUE ARI D 62
13	BC4	SOFTWARE	DT B:9 , DC D:54 , CPH D:63 , CDR D:65 , HOH D:283 , HOH D:448 , HOH D:449	BINDING SITE FOR RESIDUE CDR D 64
14	BC5	SOFTWARE	ARI C:72 , CPH C:73 , DA D:55 , CDR D:64 , ERI D:66 , HOH D:449	BINDING SITE FOR RESIDUE CDR D 65
15	BC6	SOFTWARE	DG C:43 , DG C:44 , 1GL C:71 , ARI C:72 , CPH C:73 , DA D:55 , DA D:56 , CDR D:65 , HOH D:211	BINDING SITE FOR RESIDUE ERI D 66
16	BC7	SOFTWARE	DT A:1 , DG C:44 , DC C:45 , ARI C:72 , ERI D:66	BINDING SITE FOR RESIDUE 1GL C 71
17	BC8	SOFTWARE	DT C:41 , 1GL C:71 , CPH C:73 , CDR D:65 , ERI D:66	BINDING SITE FOR RESIDUE ARI C 72
18	BC9	SOFTWARE	CPH A:33 , CDR B:34 , DC C:46 , CPH C:73 , CDR C:75	BINDING SITE FOR RESIDUE CDR C 74
19	CC1	SOFTWARE	CPH B:23 , CDR C:74 , ERI C:76 , ARI D:62 , CPH D:63	BINDING SITE FOR RESIDUE CDR C 75
20	CC2	SOFTWARE	HOH B:463 , DA C:48 , CDR C:75 , HOH C:259 , DG D:51 , DG D:52 , ARI D:62 , CPH D:63	BINDING SITE FOR RESIDUE ERI C 76
21	CC3	SOFTWARE	CPH A:33 , HOH A:481 , CPH B:23 , HOH B:480	BINDING SITE FOR RESIDUE MG A 81
22	CC4	SOFTWARE	CPH C:73 , CPH D:63 , HOH D:482 , HOH D:483	BINDING SITE FOR RESIDUE MG D 82
23	CC5	SOFTWARE	DC A:6 , CPH A:33 , MG A:81 , HOH A:481 , DG B:11 , DG B:12 , DC B:13 , DC B:14 , DA B:15 , ARI B:22 , CDR B:24 , CDR B:35 , ERI B:36 , HOH B:251 , HOH B:350 , HOH B:351 , HOH B:431 , HOH B:456 , HOH B:480 , DA C:47 , DA C:48 , CDR C:75 , HOH C:455	BINDING SITE FOR RESIDUE CPH B 23
24	CC6	SOFTWARE	DG A:3 , DG A:4 , DC A:5 , DC A:6 , ARI A:32 , MG A:81 , DC B:14 , CPH B:23 , CDR B:25 , ERI B:26 , CDR B:34 , HOH B:314 , HOH B:359 , HOH B:480 , CDR C:74	BINDING SITE FOR RESIDUE CPH A 33
25	CC7	SOFTWARE	DA A:8 , CDR B:34 , DC C:46 , CPH C:73 , CDR C:75 , ERI C:76 , DG D:52 , DC D:53 , DC D:54 , DA D:55 , ARI D:62 , CDR D:64 , MG D:82 , HOH D:283 , HOH D:315 , HOH D:482 , HOH D:483	BINDING SITE FOR RESIDUE CPH D 63
26	CC8	SOFTWARE	CDR B:24 , CDR B:25 , DG C:43 , DG C:44 , DC C:45 , DC C:46 , ARI C:72 , CDR C:74 , HOH C:227 , HOH C:230 , HOH C:298 , HOH C:427 , DC D:54 , CPH D:63 , CDR D:65 , ERI D:66 , MG D:82 , HOH D:482 , HOH D:483	BINDING SITE FOR RESIDUE CPH C 73

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:8
                                       
                  1vaq A  1 TTGGCCAA  8

Chain B from PDB  Type:DNA  Length:8
                                       
                  1vaq B  9 TTGGCCAA 16

Chain C from PDB  Type:DNA  Length:8
                                       
                  1vaq C 41 TTGGCCAA 48

Chain D from PDB  Type:DNA  Length:8
                                       
                  1vaq D 49 TTGGCCAA 56

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		1GL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ARI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CDR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CPH	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ERI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vaq)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1vaq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP \| HSSP
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description