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- PDB-1cp8: NMR STRUCTURE OF DNA (5'-D(TTGGCCAA)2-3') COMPLEXED WITH NOVEL AN... -

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Entry
Database: PDB / ID: 1cp8
TitleNMR STRUCTURE OF DNA (5'-D(TTGGCCAA)2-3') COMPLEXED WITH NOVEL ANTITUMOR DRUG UCH9
ComponentsDNA (5'-D(P*TP*TP*GP*GP*CP*CP*AP*A)-3')
KeywordsDNA
Function / homologybeta-D-Olivopyranose / Chem-DXA / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsKatahira, R. / Katahira, M. / Yamashita, Y. / Ogawa, H. / Kyogoku, Y. / Yoshida, M.
CitationJournal: Nucleic Acids Res. / Year: 1998
Title: Solution structure of the novel antitumor drug UCH9 complexed with d(TTGGCCAA)2 as determined by NMR.
Authors: Katahira, R. / Katahira, M. / Yamashita, Y. / Ogawa, H. / Kyogoku, Y. / Yoshida, M.
History
DepositionJun 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*TP*TP*GP*GP*CP*CP*AP*A)-3')
B: DNA (5'-D(P*TP*TP*GP*GP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1409
Polymers4,8532
Non-polymers2,2877
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: DNA chain DNA (5'-D(P*TP*TP*GP*GP*CP*CP*AP*A)-3')


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: TWO MOLECULES OF THE DRUG UCH9 (DDA-DXA-DDA-DDL-DRI-DDA) BOUND IN THE MINOR GROOVE THE MODEL CONTAINS TWO MOLECULES OF UCH9 AND ONE MG CATION WHICH IS COORDINATED TO TWO UCH9 MOLECULES. IN ...Details: TWO MOLECULES OF THE DRUG UCH9 (DDA-DXA-DDA-DDL-DRI-DDA) BOUND IN THE MINOR GROOVE THE MODEL CONTAINS TWO MOLECULES OF UCH9 AND ONE MG CATION WHICH IS COORDINATED TO TWO UCH9 MOLECULES. IN THIS ENTRY UCH9 IS PRESENTED AS HET GROUP, DDA-DXA-DDA-DDL-DRI-DDA. THESE GROUPS ARE NUMBERED 1-6 FOR ONE UCH9 AND 7-12 FOR THE OTHER UCH9.
#2: Polysaccharide beta-D-Olivopyranose-(1-3)-2,6-dideoxy-4-O-methyl-beta-D-glucopyranose-(1-3)-2,6-dideoxy-beta-D- ...beta-D-Olivopyranose-(1-3)-2,6-dideoxy-4-O-methyl-beta-D-glucopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta-D-Olivopyranose


Type: oligosaccharide / Mass: 552.609 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: UCH9 WAS ISOLATED FROM STREPTOMYCES SP. THE DETAILS ARE SHOWN IN THE FOLLOWING PAPER: J. ANTIBIOTICS 51, 261-266,
DescriptorTypeProgram
WURCS=2.0/3,4,3/[ad122m-1b_1-5][ad112m-1b_1-5][ad122m-1b_1-5_4*OC]/1-2-3-1/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2-deoxy-Fucp]{[(3+1)][b-D-2,6-deoxy-Glcp4Me]{[(3+1)][b-D-2,6-deoxy-Glcp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-DDA / beta-D-Olivopyranose / beta-D-Olivose / 2,6-dideoxy-beta-D-arabino-hexopyranose / 2,6-dideoxy-beta-D-glucopyranose / 2,6-dideoxy-beta-D-mannopyranose / 2-deoxy-beta-D-quinovopyranose / 2-deoxy-beta-D-rhamnoopyranose / D-Olivose / Olivose / 2,6-DIDEOXY-BETA-D-GLUCOSE / 2,6-DIDEOXY-BETA-D-MANNOSE


Type: D-saccharide, beta linking / Mass: 148.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O4
Details: UCH9 WAS ISOLATED FROM STREPTOMYCES SP. THE DETAILS ARE SHOWN IN THE FOLLOWING PAPER: J. ANTIBIOTICS 51, 261-266,
IdentifierTypeProgram
DOlibCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-OlivopyranoseCOMMON NAMEGMML 1.0
b-D-2,6-deoxy-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
OliSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-DXA / 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYDROXY-7-(SEC-BUTYL)-ANTHRACENE


Mass: 430.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30O7
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
141E.COSY
NMR detailsText: BEST STRUCTURE

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Sample preparation

DetailsContents: 10% WATER/90% D2O, 100% D2O
Sample conditionspH: 6.9 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX500 / Manufacturer: Bruker / Model: DMX500 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE ABSOLUTE CONFIGURATION OF THE HYDROPHILIC SIDECHAIN HAS NOT BEEN DETERMINED. IN THIS MODEL, IT WAS SET TO THE SAME ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE ABSOLUTE CONFIGURATION OF THE HYDROPHILIC SIDECHAIN HAS NOT BEEN DETERMINED. IN THIS MODEL, IT WAS SET TO THE SAME CONFIGURATION AS THAT OF THE OTHER AUREOLIC ACID GROUP COMPOUNDS, SUCH AS CHROMOMYCIN A3.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers submitted total number: 1

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