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- PDB-1pik: ESPERAMICIN A1-DNA COMPLEX, NMR, 4 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1pik
TitleESPERAMICIN A1-DNA COMPLEX, NMR, 4 STRUCTURES
ComponentsDNA (5'-D(C*GP*GP*AP*TP*CP*CP*GP)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DRUG COMPLEX
Function / homology2-deoxy-alpha-L-fucopyranose / Chem-DPA / Chem-MTC / Chem-TMR / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsKumar, R.A. / Ikemoto, N. / Patel, D.J.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Solution Structure of the Esperamicin A1-DNA Complex
Authors: Kumar, R.A. / Ikemoto, N. / Patel, D.J.
#1: Journal: J.Am.Chem.Soc. / Year: 1994
Title: Esperamicin A1 Intercalates Into Duplex DNA from the Minor Groove
Authors: Ikemoto, N. / Kumar, R.A. / Dedon, P.C. / Danishefsky, S.J. / Patel, D.J.
History
DepositionDec 11, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.1May 1, 2024Group: 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(C*GP*GP*AP*TP*CP*CP*GP)-3')
B: DNA (5'-D(C*GP*GP*AP*TP*CP*CP*GP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1897
Polymers4,8552
Non-polymers1,3345
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4
Representative

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Components

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DNA chain , 1 types, 2 molecules AB

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


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COMPLEXED WITH ESPERAMICIN A1

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Sugars , 3 types, 3 molecules

#2: Polysaccharide 2,4-dideoxy-3-O-methyl-4-(propan-2-ylamino)-alpha-L-threo-pentopyranose-(1-2)-4-amino-4,6-dideoxy- ...2,4-dideoxy-3-O-methyl-4-(propan-2-ylamino)-alpha-L-threo-pentopyranose-(1-2)-4-amino-4,6-dideoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 334.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122m-1b_1-5_4*N][ad21h-1a_1-5_3*OC_4*NCC/3C]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-6-deoxy-Glcp4N]{[(2+1)][a-L-2-deoxy-Xylp3Me4N]{[(4+1)][<C3>]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-TMR / 2,6-dideoxy-4-S-methyl-4-thio-beta-D-ribo-hexopyranose / 2,6-DIDEOXY-4-THIOMETHYL-BETA-D-RIBOHEXOPYRANOSIDE / 2,6-dideoxy-4-S-methyl-4-thio-beta-D-ribo-hexose / 2,6-dideoxy-4-S-methyl-4-thio-D-ribo-hexose / 2,6-dideoxy-4-S-methyl-4-thio-ribo-hexose


Type: D-saccharide, beta linking / Mass: 178.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O3S
#5: Sugar ChemComp-DLF / 2-deoxy-alpha-L-fucopyranose / 2-DEOXY-ALPHA-L-FUCOPYRANOSIDE / 2,6-dideoxy-alpha-L-lyxo-hexopyranose / 2,6-dideoxy-alpha-L-galactopyranose / 2,6-dideoxy-alpha-L-talopyranose / 2-deoxy-alpha-L-fucose / 2-deoxy-L-fucose / 2-deoxy-fucose


Type: L-saccharide, alpha linking / Mass: 148.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O4
IdentifierTypeProgram
a-L-2-deoxy-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 2 molecules

#3: Chemical ChemComp-DPA / 4,5-DIMETHOXY-N-(2'-METHOXYPROPENOYL ANTHRANILATE)


Mass: 265.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO5
#6: Chemical ChemComp-MTC / [1,8-DIHYDROXY-11-OXO-13-(2-METHYLTRITHIO-ETHYLIDENE)-BICYCLO[7.3.1]TRIDECA-4,9-DIENE-2,6-DIYN-10-YL]-CARBAMIC ACID METHYL ESTER


Mass: 407.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17NO4S3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 7 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS4001
Varian UNITYPLUSVarianUNITYPLUS5002
Varian UNITYPLUSVarianUNITYPLUS6003

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VNMRstructure solution
XEASYstructure solution
RPEAKstructure solution
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformers calculated total number: 4 / Conformers submitted total number: 4

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