data_146D # _entry.id 146D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.353 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 146D pdb_0000146d 10.2210/pdb146d/pdb WWPDB D_1000170106 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 146D _pdbx_database_status.recvd_initial_deposition_date 1993-11-09 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sastry, M.' 1 'Patel, D.J.' 2 # _citation.id primary _citation.title 'Solution structure of the mithramycin dimer-DNA complex.' _citation.journal_abbrev Biochemistry _citation.journal_volume 32 _citation.page_first 6588 _citation.page_last 6604 _citation.year 1993 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 8329387 _citation.pdbx_database_id_DOI 10.1021/bi00077a012 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sastry, M.' 1 ? primary 'Patel, D.J.' 2 ? # _cell.entry_id 146D _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 146D _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*TP*CP*GP*CP*GP*A)-3') ; 1809.217 2 ? ? ? ? 2 branched man 'beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose' 278.299 2 ? ? ? ? 3 branched syn '2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta-D-Olivopyranose' 422.468 2 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 5 non-polymer syn '1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE' 388.411 2 ? ? ? ? # _entity_name_com.entity_id 4 _entity_name_com.name MAGNESIUM # loop_ _entity_name_sys.entity_id _entity_name_sys.name 1 ;DNA (5'-D(*TP*CP*GP*CP*GP*A)-3') ; 3 '2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE' 5 '1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE' # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DT)(DC)(DG)(DC)(DG)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TCGCGA _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DC n 1 3 DG n 1 4 DC n 1 5 DG n 1 6 DA n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'CHEMICALLY SYNTHESIZED' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 146D _struct_ref.pdbx_db_accession 146D _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 146D A 1 ? 6 ? 146D 1 ? 6 ? 1 6 2 1 146D B 1 ? 6 ? 146D 7 ? 12 ? 7 12 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight CRH non-polymer . '1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE' ? 'C21 H24 O7' 388.411 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DDA 'D-saccharide, beta linking' . 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 ; 'C6 H12 O4' 148.157 DDL 'D-saccharide, beta linking' . 2,6-dideoxy-beta-D-galactopyranose ;2,6-DIDEOXY-BETA-D-GALACTOSE; 2,6-DIDEOXY-BETA-D-TALOSE; 2,6-dideoxy-beta-D-lyxo-hexopyranose; 2-deoxy-beta-D-fucopyranose; 2,6-dideoxy-D-galactose; 2,6-dideoxy-galactose ; 'C6 H12 O4' 148.157 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 MDA 'D-saccharide, beta linking' . 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose ;2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE; 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexose; 2,6-dideoxy-3-C-methyl-D-ribo-hexose; 2,6-dideoxy-3-C-methyl-ribo-hexose ; 'C7 H14 O4' 162.184 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # _pdbx_nmr_refine.entry_id 146D _pdbx_nmr_refine.method 'MOLECULAR DYNAMICS, MATRIX RELAXATION' _pdbx_nmr_refine.details ;TWO STARTING MODELS WERE OBTAINED BY DOCKING THE MG2+ COORDINATED MITHRAMYCIN DIMER IN THE MINOR GROOVE OF A AND B FORM D(TCGCGA) DUPLEX. THESE MODELS WERE SUBSEQUENTLY REFINED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. THE TWO DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL TWO STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE R FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE TWO FINAL STRUCTURES ARE: MODEL 1 MODEL 2 R FACTOR 0.146 0.136 BOND (ANGSTROMS) 0.016 0.013 ANGLES (DEGREES) 3.410 3.369. THE STRUCTURE EXHIBITS APPROXIMATE TWO-FOLD SYMMETRY, PERPENDICULAR TO THE HELICAL AXIS AND PASSING THROUGH THE MAGNESIUM IN THE COMPLEX. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 1 WHEN APPLIED TO CHAIN A OF MODEL 1. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 2 WHEN APPLIED TO CHAIN A OF MODEL 2. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 146D _pdbx_nmr_details.text ;THE HYDROXYL PROTONS IN THE RELAXATION MATRIX REFINED STRUCTURES ARE NOT WELL DETERMINED. THE HYDROPHILIC SIDE CHAIN, THE B SUGAR RESIDUE DDA 1 AND DDA 7, AND RESIDUES T 1 AND C 2 ARE UNDETERMINED. ; # _pdbx_nmr_ensemble.entry_id 146D _pdbx_nmr_ensemble.conformers_calculated_total_number 2 _pdbx_nmr_ensemble.conformers_submitted_total_number 2 _pdbx_nmr_ensemble.conformer_selection_criteria 'all calculated structures submitted' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_software.name X-PLOR _pdbx_nmr_software.version 2.1 _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors Brunger _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 146D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 146D _struct.title 'SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 146D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, MITHRAMYCIN DIMER' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 2 ? F N N 3 ? G N N 4 ? H N N 5 ? I N N 5 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? H CRH . C6 ? ? ? 1_555 C DDA . O1 ? ? A CRH 9 C DDA 1 1_555 ? ? ? ? ? ? ? 1.393 ? ? covale2 covale one ? H CRH . C2 ? ? ? 1_555 D DDA . O1 ? ? A CRH 9 D DDA 1 1_555 ? ? ? ? ? ? ? 1.429 ? ? covale3 covale one ? I CRH . C6 ? ? ? 1_555 E DDA . O1 ? ? B CRH 3 E DDA 1 1_555 ? ? ? ? ? ? ? 1.392 ? ? covale4 covale one ? I CRH . C2 ? ? ? 1_555 F DDA . O1 ? ? B CRH 3 F DDA 1 1_555 ? ? ? ? ? ? ? 1.428 ? ? covale5 covale both ? C DDA . O3 ? ? ? 1_555 C DDA . C1 ? ? C DDA 1 C DDA 2 1_555 ? ? ? ? ? ? ? 1.430 sing ? covale6 covale both ? D DDA . O3 ? ? ? 1_555 D DDL . C1 ? ? D DDA 1 D DDL 2 1_555 ? ? ? ? ? ? ? 1.432 sing ? covale7 covale both ? D DDL . O3 ? ? ? 1_555 D MDA . C1 ? ? D DDL 2 D MDA 3 1_555 ? ? ? ? ? ? ? 1.437 sing ? covale8 covale both ? E DDA . O3 ? ? ? 1_555 E DDA . C1 ? ? E DDA 1 E DDA 2 1_555 ? ? ? ? ? ? ? 1.431 sing ? covale9 covale both ? F DDA . O3 ? ? ? 1_555 F DDL . C1 ? ? F DDA 1 F DDL 2 1_555 ? ? ? ? ? ? ? 1.431 sing ? covale10 covale both ? F DDL . O3 ? ? ? 1_555 F MDA . C1 ? ? F DDL 2 F MDA 3 1_555 ? ? ? ? ? ? ? 1.436 sing ? metalc1 metalc ? ? H CRH . O9 ? ? ? 1_555 G MG . MG ? ? A CRH 9 A MG 13 1_555 ? ? ? ? ? ? ? 2.134 ? ? metalc2 metalc ? ? H CRH . O1 ? ? ? 1_555 G MG . MG ? ? A CRH 9 A MG 13 1_555 ? ? ? ? ? ? ? 2.377 ? ? metalc3 metalc ? ? G MG . MG ? ? ? 1_555 I CRH . O9 ? ? A MG 13 B CRH 3 1_555 ? ? ? ? ? ? ? 2.132 ? ? metalc4 metalc ? ? G MG . MG ? ? ? 1_555 I CRH . O1 ? ? A MG 13 B CRH 3 1_555 ? ? ? ? ? ? ? 2.378 ? ? hydrog1 hydrog ? ? A DT 1 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 1 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 1 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 2 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 2 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 2 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 3 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 3 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 3 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 5 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 5 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 5 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 1 N3 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 1 O4 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _database_PDB_matrix.entry_id 146D _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 146D _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H MG N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DT 1 1 1 DT T A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DA 6 6 6 DA A A . n B 1 1 DT 1 7 7 DT T B . n B 1 2 DC 2 8 8 DC C B . n B 1 3 DG 3 9 9 DG G B . n B 1 4 DC 4 10 10 DC C B . n B 1 5 DG 5 11 11 DG G B . n B 1 6 DA 6 12 12 DA A B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code G 4 MG 1 13 13 MG MG A . H 5 CRH 1 9 9 CRH CRH A . I 5 CRH 1 3 3 CRH CRH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O9 ? H CRH . ? A CRH 9 ? 1_555 MG ? G MG . ? A MG 13 ? 1_555 O1 ? H CRH . ? A CRH 9 ? 1_555 70.2 ? 2 O9 ? H CRH . ? A CRH 9 ? 1_555 MG ? G MG . ? A MG 13 ? 1_555 O9 ? I CRH . ? B CRH 3 ? 1_555 179.8 ? 3 O1 ? H CRH . ? A CRH 9 ? 1_555 MG ? G MG . ? A MG 13 ? 1_555 O9 ? I CRH . ? B CRH 3 ? 1_555 109.8 ? 4 O9 ? H CRH . ? A CRH 9 ? 1_555 MG ? G MG . ? A MG 13 ? 1_555 O1 ? I CRH . ? B CRH 3 ? 1_555 110.0 ? 5 O1 ? H CRH . ? A CRH 9 ? 1_555 MG ? G MG . ? A MG 13 ? 1_555 O1 ? I CRH . ? B CRH 3 ? 1_555 80.4 ? 6 O9 ? I CRH . ? B CRH 3 ? 1_555 MG ? G MG . ? A MG 13 ? 1_555 O1 ? I CRH . ? B CRH 3 ? 1_555 70.3 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 1995-03-31 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2020-07-29 5 'Structure model' 2 1 2022-01-19 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 4 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other 7 4 'Structure model' 'Structure summary' 8 5 'Structure model' 'Database references' 9 5 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' atom_site 2 4 'Structure model' chem_comp 3 4 'Structure model' entity 4 4 'Structure model' entity_name_com 5 4 'Structure model' entity_name_sys 6 4 'Structure model' pdbx_branch_scheme 7 4 'Structure model' pdbx_chem_comp_identifier 8 4 'Structure model' pdbx_database_status 9 4 'Structure model' pdbx_entity_branch 10 4 'Structure model' pdbx_entity_branch_descriptor 11 4 'Structure model' pdbx_entity_branch_link 12 4 'Structure model' pdbx_entity_branch_list 13 4 'Structure model' pdbx_entity_nonpoly 14 4 'Structure model' pdbx_nonpoly_scheme 15 4 'Structure model' pdbx_struct_assembly 16 4 'Structure model' pdbx_struct_conn_angle 17 4 'Structure model' pdbx_struct_oper_list 18 4 'Structure model' struct_asym 19 4 'Structure model' struct_conn 20 4 'Structure model' struct_site 21 4 'Structure model' struct_site_gen 22 5 'Structure model' chem_comp 23 5 'Structure model' database_2 24 5 'Structure model' entity_name_com # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_atom_site.B_iso_or_equiv' 2 4 'Structure model' '_atom_site.Cartn_x' 3 4 'Structure model' '_atom_site.Cartn_y' 4 4 'Structure model' '_atom_site.Cartn_z' 5 4 'Structure model' '_atom_site.auth_asym_id' 6 4 'Structure model' '_atom_site.auth_atom_id' 7 4 'Structure model' '_atom_site.auth_comp_id' 8 4 'Structure model' '_atom_site.auth_seq_id' 9 4 'Structure model' '_atom_site.label_asym_id' 10 4 'Structure model' '_atom_site.label_atom_id' 11 4 'Structure model' '_atom_site.label_comp_id' 12 4 'Structure model' '_atom_site.label_entity_id' 13 4 'Structure model' '_atom_site.type_symbol' 14 4 'Structure model' '_chem_comp.name' 15 4 'Structure model' '_chem_comp.type' 16 4 'Structure model' '_entity_name_com.entity_id' 17 4 'Structure model' '_entity_name_sys.entity_id' 18 4 'Structure model' '_entity_name_sys.name' 19 4 'Structure model' '_pdbx_database_status.process_site' 20 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 21 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 22 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 23 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 24 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 25 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 26 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 27 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 28 4 'Structure model' '_pdbx_struct_conn_angle.value' 29 4 'Structure model' '_struct_conn.conn_type_id' 30 4 'Structure model' '_struct_conn.id' 31 4 'Structure model' '_struct_conn.pdbx_dist_value' 32 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 33 4 'Structure model' '_struct_conn.pdbx_value_order' 34 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 35 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 36 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 37 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 38 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 39 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 40 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 41 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 42 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 43 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 44 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 45 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 46 5 'Structure model' '_chem_comp.pdbx_synonyms' 47 5 'Structure model' '_database_2.pdbx_DOI' 48 5 'Structure model' '_database_2.pdbx_database_accession' 49 5 'Structure model' '_entity_name_com.entity_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 X-PLOR refinement . ? 2 X-PLOR phasing . ? 3 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C5 _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 DT _pdbx_validate_rmsd_bond.auth_seq_id_1 1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 C7 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 DT _pdbx_validate_rmsd_bond.auth_seq_id_2 1 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.533 _pdbx_validate_rmsd_bond.bond_target_value 1.496 _pdbx_validate_rmsd_bond.bond_deviation 0.037 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 114.63 108.30 6.33 0.30 N 2 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 115.81 108.30 7.51 0.30 N 3 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 110.39 108.30 2.09 0.30 N 4 1 N7 A DG 3 ? ? C8 A DG 3 ? ? N9 A DG 3 ? ? 116.40 113.10 3.30 0.50 N 5 1 C8 A DG 3 ? ? N9 A DG 3 ? ? C4 A DG 3 ? ? 103.88 106.40 -2.52 0.40 N 6 1 "C4'" A DC 4 ? ? "C3'" A DC 4 ? ? "C2'" A DC 4 ? ? 96.93 102.20 -5.27 0.70 N 7 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 114.12 108.30 5.82 0.30 N 8 1 N7 A DG 5 ? ? C8 A DG 5 ? ? N9 A DG 5 ? ? 116.23 113.10 3.13 0.50 N 9 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 112.12 108.30 3.82 0.30 N 10 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 114.56 108.30 6.26 0.30 N 11 1 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 115.80 108.30 7.50 0.30 N 12 1 "O4'" B DG 9 ? ? "C1'" B DG 9 ? ? N9 B DG 9 ? ? 110.42 108.30 2.12 0.30 N 13 1 N7 B DG 9 ? ? C8 B DG 9 ? ? N9 B DG 9 ? ? 116.38 113.10 3.28 0.50 N 14 1 C8 B DG 9 ? ? N9 B DG 9 ? ? C4 B DG 9 ? ? 103.90 106.40 -2.50 0.40 N 15 1 "C4'" B DC 10 ? ? "C3'" B DC 10 ? ? "C2'" B DC 10 ? ? 96.95 102.20 -5.25 0.70 N 16 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? N1 B DC 10 ? ? 114.13 108.30 5.83 0.30 N 17 1 N7 B DG 11 ? ? C8 B DG 11 ? ? N9 B DG 11 ? ? 116.20 113.10 3.10 0.50 N 18 1 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 112.08 108.30 3.78 0.30 N 19 2 C6 A DT 1 ? ? C5 A DT 1 ? ? C7 A DT 1 ? ? 118.48 122.90 -4.42 0.60 N 20 2 "C3'" A DT 1 ? ? "O3'" A DT 1 ? ? P A DC 2 ? ? 128.87 119.70 9.17 1.20 Y 21 2 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 116.75 108.30 8.45 0.30 N 22 2 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 111.24 108.30 2.94 0.30 N 23 2 N7 A DG 3 ? ? C8 A DG 3 ? ? N9 A DG 3 ? ? 116.27 113.10 3.17 0.50 N 24 2 C8 A DG 3 ? ? N9 A DG 3 ? ? C4 A DG 3 ? ? 103.76 106.40 -2.64 0.40 N 25 2 "C4'" A DC 4 ? ? "C3'" A DC 4 ? ? "C2'" A DC 4 ? ? 96.47 102.20 -5.73 0.70 N 26 2 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 114.84 108.30 6.54 0.30 N 27 2 N7 A DG 5 ? ? C8 A DG 5 ? ? N9 A DG 5 ? ? 116.21 113.10 3.11 0.50 N 28 2 "C5'" A DA 6 ? ? "C4'" A DA 6 ? ? "O4'" A DA 6 ? ? 119.43 109.80 9.63 1.10 N 29 2 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 113.40 108.30 5.10 0.30 N 30 2 C6 B DT 7 ? ? C5 B DT 7 ? ? C7 B DT 7 ? ? 118.58 122.90 -4.32 0.60 N 31 2 "C3'" B DT 7 ? ? "O3'" B DT 7 ? ? P B DC 8 ? ? 128.80 119.70 9.10 1.20 Y 32 2 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 116.81 108.30 8.51 0.30 N 33 2 "O4'" B DG 9 ? ? "C1'" B DG 9 ? ? N9 B DG 9 ? ? 111.26 108.30 2.96 0.30 N 34 2 N7 B DG 9 ? ? C8 B DG 9 ? ? N9 B DG 9 ? ? 116.36 113.10 3.26 0.50 N 35 2 C8 B DG 9 ? ? N9 B DG 9 ? ? C4 B DG 9 ? ? 103.76 106.40 -2.64 0.40 N 36 2 "C4'" B DC 10 ? ? "C3'" B DC 10 ? ? "C2'" B DC 10 ? ? 96.56 102.20 -5.64 0.70 N 37 2 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? N1 B DC 10 ? ? 114.85 108.30 6.55 0.30 N 38 2 N7 B DG 11 ? ? C8 B DG 11 ? ? N9 B DG 11 ? ? 116.15 113.10 3.05 0.50 N 39 2 "C5'" B DA 12 ? ? "C4'" B DA 12 ? ? "O4'" B DA 12 ? ? 119.46 109.80 9.66 1.10 N 40 2 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 113.28 108.30 4.98 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DC A 4 ? ? 0.074 'SIDE CHAIN' 2 1 DA A 6 ? ? 0.058 'SIDE CHAIN' 3 1 DC B 10 ? ? 0.074 'SIDE CHAIN' 4 1 DA B 12 ? ? 0.058 'SIDE CHAIN' # _ndb_struct_conf_na.entry_id 146D _ndb_struct_conf_na.feature 'double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DT 1 1_555 B DA 6 1_555 -0.393 0.099 0.275 -43.852 -5.404 3.385 1 A_DT1:DA12_B A 1 ? B 12 ? 20 1 1 A DC 2 1_555 B DG 5 1_555 0.694 -0.188 0.558 -28.009 0.013 -2.266 2 A_DC2:DG11_B A 2 ? B 11 ? 19 1 1 A DG 3 1_555 B DC 4 1_555 -0.423 -0.192 0.385 8.110 -4.309 -2.903 3 A_DG3:DC10_B A 3 ? B 10 ? 19 1 1 A DC 4 1_555 B DG 3 1_555 0.452 -0.197 0.382 -8.246 -4.238 -2.901 4 A_DC4:DG9_B A 4 ? B 9 ? 19 1 1 A DG 5 1_555 B DC 2 1_555 -0.658 -0.207 0.555 27.809 0.106 -2.288 5 A_DG5:DC8_B A 5 ? B 8 ? 19 1 1 A DA 6 1_555 B DT 1 1_555 0.417 0.078 0.273 43.833 -5.265 3.443 6 A_DA6:DT7_B A 6 ? B 7 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DT 1 1_555 B DA 6 1_555 A DC 2 1_555 B DG 5 1_555 -0.722 -0.596 3.106 1.495 -4.166 30.598 -0.346 1.631 3.120 -7.843 -2.815 30.909 1 AA_DT1DC2:DG11DA12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DC 2 1_555 B DG 5 1_555 A DG 3 1_555 B DC 4 1_555 0.159 -0.631 2.224 4.743 7.197 24.927 -2.653 0.488 1.964 16.073 -10.592 26.352 2 AA_DC2DG3:DC10DG11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DG 3 1_555 B DC 4 1_555 A DC 4 1_555 B DG 3 1_555 -0.001 -0.968 3.953 0.008 -10.528 40.717 0.012 0.002 4.069 -14.834 -0.011 42.000 3 AA_DG3DC4:DG9DC10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DC 4 1_555 B DG 3 1_555 A DG 5 1_555 B DC 2 1_555 -0.160 -0.628 2.228 -4.708 7.204 24.961 -2.646 -0.478 1.970 16.070 10.502 26.381 4 AA_DC4DG5:DC8DG9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DG 5 1_555 B DC 2 1_555 A DA 6 1_555 B DT 1 1_555 0.722 -0.597 3.102 -1.534 -4.114 30.548 -0.357 -1.641 3.115 -7.757 2.892 30.854 5 AA_DG5DA6:DT7DC8_BB A 5 ? B 8 ? A 6 ? B 7 ? # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero C 2 DDA 1 C DDA 1 ? DDA 8 n C 2 DDA 2 C DDA 2 ? DDA 7 n D 3 DDA 1 D DDA 1 ? DDA 10 n D 3 DDL 2 D DDL 2 ? DDL 11 n D 3 MDA 3 D MDA 3 ? MDA 12 n E 2 DDA 1 E DDA 1 ? DDA 2 n E 2 DDA 2 E DDA 2 ? DDA 1 n F 3 DDA 1 F DDA 1 ? DDA 4 n F 3 DDL 2 F DDL 2 ? DDL 5 n F 3 MDA 3 F MDA 3 ? MDA 6 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier DDA 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DOlib DDA 'COMMON NAME' GMML 1.0 b-D-Olivopyranose DDA 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-2,6-deoxy-Glcp DDA 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Oli DDL 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-2-deoxy-Fucp # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 2 DOlib1-3DOlib1-ROH 'Glycam Condensed Sequence' GMML 1.0 2 2 'WURCS=2.0/1,2,1/[ad122m-1b_1-5]/1-1/a3-b1' WURCS PDB2Glycan 1.1.0 3 2 '[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2,6-deoxy-Glcp]{}}' LINUCS PDB-CARE ? 4 3 'WURCS=2.0/3,3,2/[ad122m-1b_1-5][ad112m-1b_1-5][ad622m-1b_1-5_3*C]/1-2-3/a3-b1_b3-c1' WURCS PDB2Glycan 1.1.0 5 3 '[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2-deoxy-Fucp]{[(3+1)][b-D-2,6-deoxy-Allp]{}}}' LINUCS PDB-CARE ? # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.value_order _pdbx_entity_branch_link.details 1 2 2 DDA C1 O1 1 DDA O3 HO3 sing ? 2 3 2 DDL C1 O1 1 DDA O3 HO3 sing ? 3 3 3 MDA C1 O1 2 DDL O3 HO3 sing ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 DDA 1 n 2 DDA 2 n 3 DDA 1 n 3 DDL 2 n 3 MDA 3 n # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'MAGNESIUM ION' MG 5 '1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE' CRH #