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- PDB-185d: SEQUENCE SPECIFICITY OF QUINOXALINE ANTIBIOTICS. 1. SOLUTION STRU... -

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Basic information

Entry
Database: PDB / ID: 185d
TitleSEQUENCE SPECIFICITY OF QUINOXALINE ANTIBIOTICS. 1. SOLUTION STRUCTURE OF A 1:1 COMPLEX BETWEEN TRIOSTIN A AND [D(GACGTC)]2 AND COMPARISON WITH THE SOLUTION STRUCTURE OF THE [N-MECYS3, N-MECYS7]TANDEM-[D(GATATC)]2 COMPLEX
Components
  • DNA (5'-D(*GP*AP*CP*GP*TP*C)-3')
  • TRIOSTIN A
KeywordsDNA/ANTIBIOTIC / BISINTERCALATOR / DEPSIPEPTIDE / QUINOXALINE / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX
Function / homologyTRIOSTIN A / 2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciesSTREPTOMYCINEAE (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, MOLECULAR DYNAMICS
AuthorsAddess, K.J. / Feigon, J.
Citation
Journal: Biochemistry / Year: 1994
Title: Sequence Specificity of Quinoxaline Antibiotics. 1. Solution Structure of a 1:1 Complex between Triostin a and [D(Gacgtc)]2 and Comparison with the Solution Structure of the [N-Mecys3,N-Mecys7] ...Title: Sequence Specificity of Quinoxaline Antibiotics. 1. Solution Structure of a 1:1 Complex between Triostin a and [D(Gacgtc)]2 and Comparison with the Solution Structure of the [N-Mecys3,N-Mecys7]Tandem-[D(Gatatc)]2 Complex.
Authors: Addess, K.J. / Feigon, J.
#1: Journal: Biochemistry / Year: 1993
Title: Solution Structure of a Complex between [N-Mecys3,N-Mecys7]Tandem and [D(Gatatc)]2
Authors: Addess, K.J. / Sinsheimer, J.S. / Feigon, J.
History
DepositionAug 10, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Feb 27, 2013Group: Other
Revision 1.5Nov 1, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly / pdbx_validate_polymer_linkage
Item: _pdbx_database_status.process_site / _pdbx_struct_assembly.method_details
Revision 1.6Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIOSTIN A
C: DNA (5'-D(*GP*AP*CP*GP*TP*C)-3')
D: DNA (5'-D(*GP*AP*CP*GP*TP*C)-3')
A: 2-CARBOXYQUINOXALINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7625
Polymers4,4133
Non-polymers3482
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-3 kcal/mol
Surface area2840 Å2
MethodPISA
Atom site foot note1: SER A 2 AND SER B 7 OF EACH MODEL ARE D-SERINE.
2: CYS A 4 AND VAL A 5 OF EACH MODEL ARE METHYLATED. CYS B 9 AND VAL B 10 OF EACH MODEL ARE METHYLATED.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / -
Representative

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Components

#1: Protein/peptide TRIOSTIN A


Type: Cyclic depsipeptide / Class: Anticancer / Mass: 794.982 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE ...Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
Source: (synth.) STREPTOMYCINEAE (bacteria) / Keywords: DEOXYRIBONUCLEIC ACID / References: NOR: NOR01129, TRIOSTIN A
#2: DNA chain DNA (5'-D(*GP*AP*CP*GP*TP*C)-3')


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Anticancer / Mass: 174.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O2
Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE ...Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
References: TRIOSTIN A
Compound detailsTRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ...TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, TRIOSTIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) QUI
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: TRIOSTIN A CONTAINS TWO PLANAR AROMATIC QUINOXALINE RINGS THAT ARE COVALENTLY ATTACHED TO A CYCLIC OCTADEPSIPEPTIDE RING REPRESENTED BY CHAINS A AND B IN THIS ENTRY. THERE IS A DISULFIDE BRIDGE ...Text: TRIOSTIN A CONTAINS TWO PLANAR AROMATIC QUINOXALINE RINGS THAT ARE COVALENTLY ATTACHED TO A CYCLIC OCTADEPSIPEPTIDE RING REPRESENTED BY CHAINS A AND B IN THIS ENTRY. THERE IS A DISULFIDE BRIDGE LINKING CYS A 4 TO CYS B 9. BOTH CYS AND VAL RESIDUES CONTAIN METHYLATED AMIDE NITROGENS; THE TWO D-SER RESIDUES ARE AMIDE BONDED TO THE TWO QUINOXALINE RINGS.

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: DISTANCE GEOMETRY, MOLECULAR DYNAMICS / Software ordinal: 1
Details: NUMBER OF ATOMS PRESENT IN ENTRY. NUMBER OF PROTEIN ATOMS 328 NUMBER OF NUCLEIC ACID ATOMS 48 NUMBER OF SOLVENT ATOMS 240 NUMBER OF HETEROGEN ATOMS 40 AVERAGE PAIRWISE RMSD BOND DISTANCES ...Details: NUMBER OF ATOMS PRESENT IN ENTRY. NUMBER OF PROTEIN ATOMS 328 NUMBER OF NUCLEIC ACID ATOMS 48 NUMBER OF SOLVENT ATOMS 240 NUMBER OF HETEROGEN ATOMS 40 AVERAGE PAIRWISE RMSD BOND DISTANCES FOR HEAVY ATOM POSITIONS FOR 5 STRUCTURES: 1.37 ANGSTROMS.
NMR ensembleConformers submitted total number: 5

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