data_306D # _entry.id 306D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 306D pdb_0000306d 10.2210/pdb306d/pdb RCSB GDLB51 ? ? WWPDB D_1000178774 ? ? # 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 1997-09-22 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-21 5 'Structure model' 1 4 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # 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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Refinement description' # 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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site 7 5 'Structure model' pdbx_initial_refinement_model # 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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 31 4 'Structure model' '_struct_conn.ptnr2_symmetry' 32 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 306D _pdbx_database_status.recvd_initial_deposition_date 1997-01-03 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Chen, X.' 1 'Ramakrishnan, B.' 2 'Sundaralingam, M.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC).' J.Mol.Biol. 267 1157 1170 1997 JMOBAK UK 0022-2836 0070 ? 9150404 10.1006/jmbi.1997.0941 1 'Binding of two Distamycin A Molecules in the Minor Groove of an Alternating B-DNA' Nat.Struct.Biol. 1 169 175 1994 NSBIEW US 1072-8368 2024 ? ? ? 2 'Crystal Structures of B-Form DNA-RNA Chimers Complexed with Distamycin' Nat.Struct.Biol. 2 733 735 1995 NSBIEW US 1072-8368 2024 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chen, X.' 1 ? primary 'Ramakrishnan, B.' 2 ? primary 'Sundaralingam, M.' 3 ? 1 'Chen, X.' 4 ? 1 'Ramakrishnan, B.' 5 ? 1 'Rao, S.T.' 6 ? 1 'Sundaralingam, M.' 7 ? 2 'Chen, X.' 8 ? 2 'Ramakrishnan, B.' 9 ? 2 'Sundaralingam, M.' 10 ? # 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(*IP*CP*IP*TP*AP*CP*IP*C)-3') ; 2382.563 1 ? ? ? ? 2 non-polymer syn 'DISTAMYCIN A' 481.508 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 62 ? ? ? ? # _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 '(DI)(DC)(DI)(DT)(DA)(DC)(DI)(DC)' _entity_poly.pdbx_seq_one_letter_code_can ICITACIC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'DISTAMYCIN A' DMY 3 'MAGNESIUM ION' MG 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DI n 1 2 DC n 1 3 DI n 1 4 DT n 1 5 DA n 1 6 DC n 1 7 DI n 1 8 DC n # 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 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 DI 'DNA linking' y "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" ? 'C10 H13 N4 O7 P' 332.207 DMY non-polymer . 'DISTAMYCIN A' 'DISTAMYCIN; STALLIMYCIN' 'C22 H27 N9 O4' 481.508 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 DI 1 1 1 DI I A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DI 3 3 3 DI I A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DI 7 7 7 DI I A . n A 1 8 DC 8 8 8 DC C A . 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 B 2 DMY 1 9 9 DMY DMY A . C 3 MG 1 10 10 MG MG A . D 4 HOH 1 11 11 HOH HOH A . D 4 HOH 2 12 12 HOH HOH A . D 4 HOH 3 13 13 HOH HOH A . D 4 HOH 4 14 14 HOH HOH A . D 4 HOH 5 15 15 HOH HOH A . D 4 HOH 6 16 16 HOH HOH A . D 4 HOH 7 17 17 HOH HOH A . D 4 HOH 8 18 18 HOH HOH A . D 4 HOH 9 19 19 HOH HOH A . D 4 HOH 10 20 20 HOH HOH A . D 4 HOH 11 21 21 HOH HOH A . D 4 HOH 12 22 22 HOH HOH A . D 4 HOH 13 23 23 HOH HOH A . D 4 HOH 14 24 24 HOH HOH A . D 4 HOH 15 25 25 HOH HOH A . D 4 HOH 16 26 26 HOH HOH A . D 4 HOH 17 27 27 HOH HOH A . D 4 HOH 18 28 28 HOH HOH A . D 4 HOH 19 29 29 HOH HOH A . D 4 HOH 20 30 30 HOH HOH A . D 4 HOH 21 31 31 HOH HOH A . D 4 HOH 22 32 32 HOH HOH A . D 4 HOH 23 33 33 HOH HOH A . D 4 HOH 24 34 34 HOH HOH A . D 4 HOH 25 35 35 HOH HOH A . D 4 HOH 26 36 36 HOH HOH A . D 4 HOH 27 37 37 HOH HOH A . D 4 HOH 28 38 38 HOH HOH A . D 4 HOH 29 39 39 HOH HOH A . D 4 HOH 30 40 40 HOH HOH A . D 4 HOH 31 41 41 HOH HOH A . D 4 HOH 32 42 42 HOH HOH A . D 4 HOH 33 43 43 HOH HOH A . D 4 HOH 34 44 44 HOH HOH A . D 4 HOH 35 45 45 HOH HOH A . D 4 HOH 36 46 46 HOH HOH A . D 4 HOH 37 47 47 HOH HOH A . D 4 HOH 38 48 48 HOH HOH A . D 4 HOH 39 49 49 HOH HOH A . D 4 HOH 40 50 50 HOH HOH A . D 4 HOH 41 51 51 HOH HOH A . D 4 HOH 42 52 52 HOH HOH A . D 4 HOH 43 53 53 HOH HOH A . D 4 HOH 44 54 54 HOH HOH A . D 4 HOH 45 55 55 HOH HOH A . D 4 HOH 46 56 56 HOH HOH A . D 4 HOH 47 57 57 HOH HOH A . D 4 HOH 48 58 58 HOH HOH A . D 4 HOH 49 59 59 HOH HOH A . D 4 HOH 50 60 60 HOH HOH A . D 4 HOH 51 61 61 HOH HOH A . D 4 HOH 52 62 62 HOH HOH A . D 4 HOH 53 63 63 HOH HOH A . D 4 HOH 54 64 64 HOH HOH A . D 4 HOH 55 65 65 HOH HOH A . D 4 HOH 56 66 66 HOH HOH A . D 4 HOH 57 67 67 HOH HOH A . D 4 HOH 58 68 68 HOH HOH A . D 4 HOH 59 69 69 HOH HOH A . D 4 HOH 60 70 70 HOH HOH A . D 4 HOH 61 71 71 HOH HOH A . D 4 HOH 62 72 72 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal XENGEN 'data collection' 2.0 ? 1 XENGEN 'data reduction' 2.0 ? 2 X-PLOR 'model building' . ? 3 X-PLOR refinement . ? 4 XENGEN 'data scaling' 'V. 2.0' ? 5 X-PLOR phasing . ? 6 # _cell.entry_id 306D _cell.length_a 28.030 _cell.length_b 28.030 _cell.length_c 58.040 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 306D _symmetry.space_group_name_H-M 'P 41 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 # _exptl.entry_id 306D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 46.17 _exptl_crystal.density_Matthews 2.29 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details 'ROOM TEMPERATURE' _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'NA CACODYLATE' ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 1 SPERMINE_HCL ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 298.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type SIEMENS-NICOLET _diffrn_detector.pdbx_collection_date 1994-02-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 306D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 5.100 _reflns.d_resolution_high 1.500 _reflns.number_obs 3778 _reflns.number_all 20233 _reflns.percent_possible_obs 92.000 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.048 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.400 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 306D _refine.ls_number_reflns_obs 2672 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 5.100 _refine.ls_d_res_high 1.600 _refine.ls_percent_reflns_obs 66.000 _refine.ls_R_factor_obs 0.153 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.153 _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 16.30 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model GDHB25 _refine.pdbx_method_to_determine_struct 'DIRECT REFINEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 158 _refine_hist.pdbx_number_atoms_ligand 36 _refine_hist.number_atoms_solvent 62 _refine_hist.number_atoms_total 256 _refine_hist.d_res_high 1.600 _refine_hist.d_res_low 5.100 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.014 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 4.40 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 38.9 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 2.50 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 306D _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 # _struct.entry_id 306D _struct.title 'SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICITACIC)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 306D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DOUBLE DRUG IN THE MINOR GROOVE, DNA' # 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 2 ? C N N 3 ? D N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 306D _struct_ref.pdbx_db_accession 306D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 306D _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 306D _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 8 # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 6_555 x,-y,-z+1/2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 29.0200000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # 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 metalc1 metalc ? ? A DC 6 OP2 ? ? ? 1_555 C MG . MG ? ? A DC 6 A MG 10 1_555 ? ? ? ? ? ? ? 1.981 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 10 A HOH 11 1_555 ? ? ? ? ? ? ? 2.056 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 10 A HOH 12 4_554 ? ? ? ? ? ? ? 2.113 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 10 A HOH 13 4_554 ? ? ? ? ? ? ? 2.245 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 10 A HOH 14 1_555 ? ? ? ? ? ? ? 2.200 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 10 A HOH 16 1_555 ? ? ? ? ? ? ? 2.130 ? ? hydrog1 hydrog ? ? A DT 4 N3 ? ? ? 1_555 A DA 5 N1 ? ? A DT 4 A DA 5 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A DT 4 A DA 5 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A DT 4 N3 ? ? A DA 5 A DT 4 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A DT 4 O4 ? ? A DA 5 A DT 4 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 OP2 ? A DC 6 ? A DC 6 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 11 ? 1_555 90.7 ? 2 OP2 ? A DC 6 ? A DC 6 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 12 ? 4_554 98.4 ? 3 O ? D HOH . ? A HOH 11 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 12 ? 4_554 92.8 ? 4 OP2 ? A DC 6 ? A DC 6 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 13 ? 4_554 167.1 ? 5 O ? D HOH . ? A HOH 11 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 13 ? 4_554 78.7 ? 6 O ? D HOH . ? A HOH 12 ? 4_554 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 13 ? 4_554 89.6 ? 7 OP2 ? A DC 6 ? A DC 6 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 14 ? 1_555 97.1 ? 8 O ? D HOH . ? A HOH 11 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 14 ? 1_555 172.1 ? 9 O ? D HOH . ? A HOH 12 ? 4_554 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 14 ? 1_555 85.3 ? 10 O ? D HOH . ? A HOH 13 ? 4_554 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 14 ? 1_555 93.6 ? 11 OP2 ? A DC 6 ? A DC 6 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 16 ? 1_555 86.2 ? 12 O ? D HOH . ? A HOH 11 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 16 ? 1_555 93.9 ? 13 O ? D HOH . ? A HOH 12 ? 4_554 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 16 ? 1_555 171.7 ? 14 O ? D HOH . ? A HOH 13 ? 4_554 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 16 ? 1_555 87.1 ? 15 O ? D HOH . ? A HOH 14 ? 1_555 MG ? C MG . ? A MG 10 ? 1_555 O ? D HOH . ? A HOH 16 ? 1_555 87.3 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A DMY 9 ? 14 'BINDING SITE FOR RESIDUE DMY A 9' AC2 Software A MG 10 ? 6 'BINDING SITE FOR RESIDUE MG A 10' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 14 DC A 2 ? DC A 2 . ? 1_555 ? 2 AC1 14 DI A 3 ? DI A 3 . ? 1_555 ? 3 AC1 14 DT A 4 ? DT A 4 . ? 6_555 ? 4 AC1 14 DA A 5 ? DA A 5 . ? 6_555 ? 5 AC1 14 DC A 6 ? DC A 6 . ? 6_555 ? 6 AC1 14 DC A 6 ? DC A 6 . ? 8_565 ? 7 AC1 14 DI A 7 ? DI A 7 . ? 6_555 ? 8 AC1 14 DC A 8 ? DC A 8 . ? 6_555 ? 9 AC1 14 HOH D . ? HOH A 15 . ? 1_555 ? 10 AC1 14 HOH D . ? HOH A 28 . ? 1_555 ? 11 AC1 14 HOH D . ? HOH A 30 . ? 1_555 ? 12 AC1 14 HOH D . ? HOH A 32 . ? 1_555 ? 13 AC1 14 HOH D . ? HOH A 33 . ? 6_555 ? 14 AC1 14 HOH D . ? HOH A 44 . ? 6_555 ? 15 AC2 6 DC A 6 ? DC A 6 . ? 1_555 ? 16 AC2 6 HOH D . ? HOH A 11 . ? 1_555 ? 17 AC2 6 HOH D . ? HOH A 12 . ? 4_554 ? 18 AC2 6 HOH D . ? HOH A 13 . ? 4_554 ? 19 AC2 6 HOH D . ? HOH A 14 . ? 1_555 ? 20 AC2 6 HOH D . ? HOH A 16 . ? 1_555 ? # 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 DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.90 108.30 2.60 0.30 N 2 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 122.85 118.90 3.95 0.60 N 3 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 110.43 108.30 2.13 0.30 N 4 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 118.66 122.90 -4.24 0.60 N 5 1 "O3'" A DA 5 ? ? P A DC 6 ? ? OP2 A DC 6 ? ? 118.50 110.50 8.00 1.10 Y 6 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 111.14 108.30 2.84 0.30 N 7 1 N1 A DC 6 ? ? C2 A DC 6 ? ? O2 A DC 6 ? ? 122.71 118.90 3.81 0.60 N 8 1 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 122.65 118.90 3.75 0.60 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 DI A 3 ? ? 0.074 'SIDE CHAIN' 2 1 DA A 5 ? ? 0.072 'SIDE CHAIN' # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DI OP3 O N N 71 DI P P N N 72 DI OP1 O N N 73 DI OP2 O N N 74 DI "O5'" O N N 75 DI "C5'" C N N 76 DI "C4'" C N R 77 DI "O4'" O N N 78 DI "C3'" C N S 79 DI "O3'" O N N 80 DI "C2'" C N N 81 DI "C1'" C N R 82 DI N9 N Y N 83 DI C8 C Y N 84 DI N7 N Y N 85 DI C5 C Y N 86 DI C6 C N N 87 DI O6 O N N 88 DI N1 N N N 89 DI C2 C N N 90 DI N3 N N N 91 DI C4 C Y N 92 DI HOP3 H N N 93 DI HOP2 H N N 94 DI "H5'" H N N 95 DI "H5''" H N N 96 DI "H4'" H N N 97 DI "H3'" H N N 98 DI "HO3'" H N N 99 DI "H2'" H N N 100 DI "H2''" H N N 101 DI "H1'" H N N 102 DI H8 H N N 103 DI H1 H N N 104 DI H2 H N N 105 DMY C1 C N N 106 DMY O1 O N N 107 DMY N1 N N N 108 DMY C2 C Y N 109 DMY C3 C Y N 110 DMY C4 C Y N 111 DMY N2 N Y N 112 DMY C5 C Y N 113 DMY C6 C N N 114 DMY C7 C N N 115 DMY O2 O N N 116 DMY N3 N N N 117 DMY C8 C Y N 118 DMY C9 C Y N 119 DMY C10 C Y N 120 DMY N4 N Y N 121 DMY C11 C Y N 122 DMY C12 C N N 123 DMY C13 C N N 124 DMY O3 O N N 125 DMY N5 N N N 126 DMY C14 C Y N 127 DMY C15 C Y N 128 DMY C16 C Y N 129 DMY N6 N Y N 130 DMY C17 C Y N 131 DMY C18 C N N 132 DMY C19 C N N 133 DMY O4 O N N 134 DMY N7 N N N 135 DMY C20 C N N 136 DMY C21 C N N 137 DMY C22 C N N 138 DMY N8 N N N 139 DMY N9 N N N 140 DMY H1 H N N 141 DMY HN1 H N N 142 DMY H3 H N N 143 DMY H5 H N N 144 DMY H61 H N N 145 DMY H62 H N N 146 DMY H63 H N N 147 DMY HN3 H N N 148 DMY H9 H N N 149 DMY H11 H N N 150 DMY H121 H N N 151 DMY H122 H N N 152 DMY H123 H N N 153 DMY HN5 H N N 154 DMY H15 H N N 155 DMY H17 H N N 156 DMY H181 H N N 157 DMY H182 H N N 158 DMY H183 H N N 159 DMY HN7 H N N 160 DMY H201 H N N 161 DMY H202 H N N 162 DMY H211 H N N 163 DMY H212 H N N 164 DMY HN8 H N N 165 DMY HN91 H N N 166 DMY HN92 H N N 167 DT OP3 O N N 168 DT P P N N 169 DT OP1 O N N 170 DT OP2 O N N 171 DT "O5'" O N N 172 DT "C5'" C N N 173 DT "C4'" C N R 174 DT "O4'" O N N 175 DT "C3'" C N S 176 DT "O3'" O N N 177 DT "C2'" C N N 178 DT "C1'" C N R 179 DT N1 N N N 180 DT C2 C N N 181 DT O2 O N N 182 DT N3 N N N 183 DT C4 C N N 184 DT O4 O N N 185 DT C5 C N N 186 DT C7 C N N 187 DT C6 C N N 188 DT HOP3 H N N 189 DT HOP2 H N N 190 DT "H5'" H N N 191 DT "H5''" H N N 192 DT "H4'" H N N 193 DT "H3'" H N N 194 DT "HO3'" H N N 195 DT "H2'" H N N 196 DT "H2''" H N N 197 DT "H1'" H N N 198 DT H3 H N N 199 DT H71 H N N 200 DT H72 H N N 201 DT H73 H N N 202 DT H6 H N N 203 HOH O O N N 204 HOH H1 H N N 205 HOH H2 H N N 206 MG MG MG N N 207 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DI OP3 P sing N N 74 DI OP3 HOP3 sing N N 75 DI P OP1 doub N N 76 DI P OP2 sing N N 77 DI P "O5'" sing N N 78 DI OP2 HOP2 sing N N 79 DI "O5'" "C5'" sing N N 80 DI "C5'" "C4'" sing N N 81 DI "C5'" "H5'" sing N N 82 DI "C5'" "H5''" sing N N 83 DI "C4'" "O4'" sing N N 84 DI "C4'" "C3'" sing N N 85 DI "C4'" "H4'" sing N N 86 DI "O4'" "C1'" sing N N 87 DI "C3'" "O3'" sing N N 88 DI "C3'" "C2'" sing N N 89 DI "C3'" "H3'" sing N N 90 DI "O3'" "HO3'" sing N N 91 DI "C2'" "C1'" sing N N 92 DI "C2'" "H2'" sing N N 93 DI "C2'" "H2''" sing N N 94 DI "C1'" N9 sing N N 95 DI "C1'" "H1'" sing N N 96 DI N9 C8 sing Y N 97 DI N9 C4 sing Y N 98 DI C8 N7 doub Y N 99 DI C8 H8 sing N N 100 DI N7 C5 sing Y N 101 DI C5 C6 sing N N 102 DI C5 C4 doub Y N 103 DI C6 O6 doub N N 104 DI C6 N1 sing N N 105 DI N1 C2 sing N N 106 DI N1 H1 sing N N 107 DI C2 N3 doub N N 108 DI C2 H2 sing N N 109 DI N3 C4 sing N N 110 DMY C1 O1 doub N N 111 DMY C1 N1 sing N N 112 DMY C1 H1 sing N N 113 DMY N1 C2 sing N N 114 DMY N1 HN1 sing N N 115 DMY C2 C3 sing Y N 116 DMY C2 C5 doub Y N 117 DMY C3 C4 doub Y N 118 DMY C3 H3 sing N N 119 DMY C4 N2 sing Y N 120 DMY C4 C7 sing N N 121 DMY N2 C5 sing Y N 122 DMY N2 C6 sing N N 123 DMY C5 H5 sing N N 124 DMY C6 H61 sing N N 125 DMY C6 H62 sing N N 126 DMY C6 H63 sing N N 127 DMY C7 O2 doub N N 128 DMY C7 N3 sing N N 129 DMY N3 C8 sing N N 130 DMY N3 HN3 sing N N 131 DMY C8 C9 sing Y N 132 DMY C8 C11 doub Y N 133 DMY C9 C10 doub Y N 134 DMY C9 H9 sing N N 135 DMY C10 N4 sing Y N 136 DMY C10 C13 sing N N 137 DMY N4 C11 sing Y N 138 DMY N4 C12 sing N N 139 DMY C11 H11 sing N N 140 DMY C12 H121 sing N N 141 DMY C12 H122 sing N N 142 DMY C12 H123 sing N N 143 DMY C13 O3 doub N N 144 DMY C13 N5 sing N N 145 DMY N5 C14 sing N N 146 DMY N5 HN5 sing N N 147 DMY C14 C15 sing Y N 148 DMY C14 C17 doub Y N 149 DMY C15 C16 doub Y N 150 DMY C15 H15 sing N N 151 DMY C16 N6 sing Y N 152 DMY C16 C19 sing N N 153 DMY N6 C17 sing Y N 154 DMY N6 C18 sing N N 155 DMY C17 H17 sing N N 156 DMY C18 H181 sing N N 157 DMY C18 H182 sing N N 158 DMY C18 H183 sing N N 159 DMY C19 O4 doub N N 160 DMY C19 N7 sing N N 161 DMY N7 C20 sing N N 162 DMY N7 HN7 sing N N 163 DMY C20 C21 sing N N 164 DMY C20 H201 sing N N 165 DMY C20 H202 sing N N 166 DMY C21 C22 sing N N 167 DMY C21 H211 sing N N 168 DMY C21 H212 sing N N 169 DMY C22 N8 doub N N 170 DMY C22 N9 sing N N 171 DMY N8 HN8 sing N N 172 DMY N9 HN91 sing N N 173 DMY N9 HN92 sing N N 174 DT OP3 P sing N N 175 DT OP3 HOP3 sing N N 176 DT P OP1 doub N N 177 DT P OP2 sing N N 178 DT P "O5'" sing N N 179 DT OP2 HOP2 sing N N 180 DT "O5'" "C5'" sing N N 181 DT "C5'" "C4'" sing N N 182 DT "C5'" "H5'" sing N N 183 DT "C5'" "H5''" sing N N 184 DT "C4'" "O4'" sing N N 185 DT "C4'" "C3'" sing N N 186 DT "C4'" "H4'" sing N N 187 DT "O4'" "C1'" sing N N 188 DT "C3'" "O3'" sing N N 189 DT "C3'" "C2'" sing N N 190 DT "C3'" "H3'" sing N N 191 DT "O3'" "HO3'" sing N N 192 DT "C2'" "C1'" sing N N 193 DT "C2'" "H2'" sing N N 194 DT "C2'" "H2''" sing N N 195 DT "C1'" N1 sing N N 196 DT "C1'" "H1'" sing N N 197 DT N1 C2 sing N N 198 DT N1 C6 sing N N 199 DT C2 O2 doub N N 200 DT C2 N3 sing N N 201 DT N3 C4 sing N N 202 DT N3 H3 sing N N 203 DT C4 O4 doub N N 204 DT C4 C5 sing N N 205 DT C5 C7 sing N N 206 DT C5 C6 doub N N 207 DT C7 H71 sing N N 208 DT C7 H72 sing N N 209 DT C7 H73 sing N N 210 DT C6 H6 sing N N 211 HOH O H1 sing N N 212 HOH O H2 sing N N 213 # 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 4 1_555 A DA 5 6_555 -0.002 -0.058 -0.148 -0.145 -7.258 -6.440 1 A_DT4:DA5_A A 4 ? A 5 ? 20 1 1 A DA 5 1_555 A DT 4 6_555 0.002 -0.058 -0.148 0.145 -7.258 -6.440 2 A_DA5:DT4_A A 5 ? A 4 ? 20 1 # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 A _ndb_struct_na_base_pair_step.i_label_comp_id_1 DT _ndb_struct_na_base_pair_step.i_label_seq_id_1 4 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 A _ndb_struct_na_base_pair_step.j_label_comp_id_1 DA _ndb_struct_na_base_pair_step.j_label_seq_id_1 5 _ndb_struct_na_base_pair_step.j_symmetry_1 6_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 DA _ndb_struct_na_base_pair_step.i_label_seq_id_2 5 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 A _ndb_struct_na_base_pair_step.j_label_comp_id_2 DT _ndb_struct_na_base_pair_step.j_label_seq_id_2 4 _ndb_struct_na_base_pair_step.j_symmetry_2 6_555 _ndb_struct_na_base_pair_step.shift 0.000 _ndb_struct_na_base_pair_step.slide 2.398 _ndb_struct_na_base_pair_step.rise 3.371 _ndb_struct_na_base_pair_step.tilt 0.000 _ndb_struct_na_base_pair_step.roll -4.912 _ndb_struct_na_base_pair_step.twist 47.722 _ndb_struct_na_base_pair_step.x_displacement 3.336 _ndb_struct_na_base_pair_step.y_displacement 0.000 _ndb_struct_na_base_pair_step.helical_rise 3.124 _ndb_struct_na_base_pair_step.inclination -6.053 _ndb_struct_na_base_pair_step.tip 0.000 _ndb_struct_na_base_pair_step.helical_twist 47.959 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_DT4DA5:DT4DA5_AA _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 4 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 A _ndb_struct_na_base_pair_step.j_auth_seq_id_1 5 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 5 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 A _ndb_struct_na_base_pair_step.j_auth_seq_id_2 4 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # _pdbx_initial_refinement_model.accession_code 159D _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details GDHB25 # _atom_sites.entry_id 306D _atom_sites.fract_transf_matrix[1][1] 0.035676 _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] 0.035676 _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] 0.017229 _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 MG N O P # loop_