Structure refinement of the chromomycin dimer-DNA oligomer complex in solution.

Gao, X.L; Mirau, P; Patel, D.J.

Macromolecule Content

Unique nucleic acid chains: 1

1D83

STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN SOLUTION

DOI: 10.2210/pdb1d83/pdb
NDB: 1D83

Classification: DNA
Deposited: 1992-07-22 Released: 1993-07-15
Deposition author(s): Gao, X., Mirau, P., Patel, D.J.

Structural Biology Knowledgebase: 1D83 SBKB.org

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: --
Conformers Submitted: 1
Selection Criteria:

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: DNA

Total Structure Weight: 7156.16

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
DNA (5'-D(APAPGPGPCPCPTPT)-3')	A, B	8	synthetic

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
CPH Query on CPH Download SDF File Download CCD File	A, B	(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10- tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen- 2-yl]-D-xylulose None (Synonym) C₂₁ H₂₄ O₉ AOCJXLJIUYHXRS-PKRZCTMMSA-N	Poseview Image of CPH in 1D83 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
ERI Query on ERI Download SDF File Download CCD File	A, B	4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L- ARABINO-HEXOPYRANOSE C₉ H₁₆ O₅ YJOQPCPEUGDGFS-VHKYIWFCSA-N	Poseview Image of ERI in 1D83 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
ARI Query on ARI Download SDF File Download CCD File	A, B	[O4]-ACETOXY-2,3-DIDEOXYFUCOSE C₈ H₁₄ O₄ NNWBJOVUTCFRGH-LPBLVHEISA-N	Poseview Image of ARI in 1D83 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
1GL Query on 1GL Download SDF File Download CCD File	A, B	4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE C₇ H₁₄ O₄ CDRBUGSWTNDUSM-JWXFUTCRSA-N	Poseview Image of 1GL in 1D83 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
CDR Query on CDR Download SDF File Download CCD File	A, B	2,3-DIDEOXYFUCOSE C₆ H₁₂ O₃ ZCYMCBOUZXAAJG-NGJCXOISSA-N	Poseview Image of CDR in 1D83 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
MG Query on MG Download SDF File Download CCD File	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N	Poseview Image of MG in 1D83 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)