data_481D # _entry.id 481D # _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 481D pdb_0000481d 10.2210/pdb481d/pdb NDB HD0001 ? ? RCSB RCSB001246 ? ? WWPDB D_1000001246 ? ? # 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 2002-04-27 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-12-27 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' diffrn_source 5 4 'Structure model' struct_conn 6 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' '_diffrn_source.pdbx_synchrotron_site' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 481D _pdbx_database_status.recvd_initial_deposition_date 1999-07-23 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _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 'Declercq, R.' 1 'Van Meervelt, L.' 2 # 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 structure of double helical hexitol nucleic acids.' J.Am.Chem.Soc. 124 928 933 2002 JACSAT US 0002-7863 0004 ? 11829600 10.1021/ja016570w 1 ;1',5'-Anhydrohexitol Nucleic Acids, a New Promising Antisense Construct ; Angew.Chem.Int.Ed.Engl. 34 1338 1342 1995 ACIEAY GE 0570-0833 0179 ? ? 10.1002/anie.199513381 2 ;1',5'-Anhydro-2',3'-Dideoxy-2'-(Guanin-9-Yl)-D-Arabino Hexitol ; 'Acta Crystallogr.,Sect.C' 52 1213 1214 1995 ACSCEE DK 0108-2701 0591 ? ? 10.1107/S0108270195015101 3 'Molecular Dynamics Simulation to Investigate Differences in Groove Hydration of HNA/RNA Hybrids as Compared to HNA/DNA Complexes' J.Am.Chem.Soc. 120 5381 ? 1998 JACSAT US 0002-7863 0004 ? ? 10.1021/ja973721f 4 ;Oligonucleotides with 1',5'-Anhydrohexitol Nucleoside Building Blocks: Crystallisation and Preliminary X-Ray Studies of h(GTGTACAC) ; 'Acta Crystallogr.,Sect.D' 55 279 ? 1999 ABCRE6 DK 0907-4449 0766 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Declercq, R.' 1 ? primary 'Van Aerschot, A.' 2 ? primary 'Read, R.J.' 3 ? primary 'Herdewijn, P.' 4 ? primary 'Van Meervelt, L.' 5 ? 1 'Van Aerschot, A.' 6 ? 1 'Verheggen, I.' 7 ? 1 'Hendrix, C.' 8 ? 1 'Herdewijn, P.' 9 ? 2 'Declercq, R.' 10 ? 2 'Herdewijn, P.' 11 ? 2 'Van Meervelt, L.' 12 ? 3 'De Winter, H.' 13 ? 3 'Lescrinier, E.' 14 ? 3 'Van Aerschot, A.' 15 ? 3 'Herdewijn, P' 16 ? 4 'Declercq, R.' 17 ? 4 'Van Aerschot, A.' 18 ? 4 'Herdewijn, P.' 19 ? 4 'Van Meervelt, L.' 20 ? # 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 "5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'" 2538.831 1 ? ? ? 'THE SUGAR MOIETIES ARE NOT DEOXYRIBOSE BUT D-ARABINO-HEXITOL' 2 water nat water 18.015 40 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(6HG)(6HT)(6HG)(6HT)(6HA)(6HC)(6HA)(6HC)' _entity_poly.pdbx_seq_one_letter_code_can GTGTACAC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 6HG n 1 2 6HT n 1 3 6HG n 1 4 6HT n 1 5 6HA n 1 6 6HC n 1 7 6HA n 1 8 6HC 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 6HA 'DNA linking' n "1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(ADENIN-9-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL" ? 'C11 H16 N5 O6 P' 345.248 6HC 'DNA linking' n "1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(CYTOSIN-1-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL" ? 'C10 H16 N3 O7 P' 321.224 6HG 'DNA linking' n "1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(GUANIN-9-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL" ? 'C11 H16 N5 O7 P' 361.248 6HT 'DNA linking' n "1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(THYMIN-1-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL" ? 'C11 H17 N2 O8 P' 336.235 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 6HG 1 1 1 6HG 6HG A . n A 1 2 6HT 2 2 2 6HT 6HT A . n A 1 3 6HG 3 3 3 6HG 6HG A . n A 1 4 6HT 4 4 4 6HT 6HT A . n A 1 5 6HA 5 5 5 6HA 6HA A . n A 1 6 6HC 6 6 6 6HC 6HC A . n A 1 7 6HA 7 7 7 6HA 6HA A . n A 1 8 6HC 8 8 8 6HC 6HC 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 HOH 1 9 9 HOH HOH A . B 2 HOH 2 10 10 HOH HOH A . B 2 HOH 3 11 11 HOH HOH A . B 2 HOH 4 12 12 HOH HOH A . B 2 HOH 5 13 13 HOH HOH A . B 2 HOH 6 14 14 HOH HOH A . B 2 HOH 7 15 15 HOH HOH A . B 2 HOH 8 16 16 HOH HOH A . B 2 HOH 9 17 17 HOH HOH A . B 2 HOH 10 18 18 HOH HOH A . B 2 HOH 11 19 19 HOH HOH A . B 2 HOH 12 20 20 HOH HOH A . B 2 HOH 13 21 21 HOH HOH A . B 2 HOH 14 22 22 HOH HOH A . B 2 HOH 15 23 23 HOH HOH A . B 2 HOH 16 24 24 HOH HOH A . B 2 HOH 17 25 25 HOH HOH A . B 2 HOH 18 26 26 HOH HOH A . B 2 HOH 19 27 27 HOH HOH A . B 2 HOH 20 28 28 HOH HOH A . B 2 HOH 21 29 29 HOH HOH A . B 2 HOH 22 30 30 HOH HOH A . B 2 HOH 23 31 31 HOH HOH A . B 2 HOH 24 32 32 HOH HOH A . B 2 HOH 25 33 33 HOH HOH A . B 2 HOH 26 34 34 HOH HOH A . B 2 HOH 27 35 35 HOH HOH A . B 2 HOH 28 36 36 HOH HOH A . B 2 HOH 29 37 37 HOH HOH A . B 2 HOH 30 39 39 HOH HOH A . B 2 HOH 31 40 40 HOH HOH A . B 2 HOH 32 41 41 HOH HOH A . B 2 HOH 33 42 42 HOH HOH A . B 2 HOH 34 43 43 HOH HOH A . B 2 HOH 35 44 44 HOH HOH A . B 2 HOH 36 45 45 HOH HOH A . B 2 HOH 37 46 46 HOH HOH A . B 2 HOH 38 47 47 HOH HOH A . B 2 HOH 39 48 48 HOH HOH A . B 2 HOH 40 49 49 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal BRUTE 'model building' . ? 1 SHELXL-97 refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 BRUTE phasing . ? 5 # _cell.entry_id 481D _cell.length_a 33.041 _cell.length_b 33.041 _cell.length_c 38.924 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 481D _symmetry.space_group_name_H-M 'P 32 1 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 153 # _exptl.entry_id 481D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 49.09 _exptl_crystal.density_Matthews 2.42 _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 ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED CACODYLATE BUFFER, KCL, BACL2, SPERMINE TETRACHLORIDE, AND MPD, pH 7.0, 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 'CACODYLATE BUFFER' ? ? ? 1 2 1 KCL ? ? ? 1 3 1 BACL2 ? ? ? 1 4 1 SPERMINE ? ? ? 1 5 1 MPD ? ? ? 1 6 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1998-10-22 _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 MIRRORS _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8375 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7B' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW7B _diffrn_source.pdbx_wavelength 0.8375 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 481D _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 1.6 _reflns.number_obs 3345 _reflns.number_all 3345 _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.0710000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 13.2 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.5 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.63 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.1730000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 6.6 _reflns_shell.pdbx_redundancy 4.4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 481D _refine.ls_number_reflns_obs 3330 _refine.ls_number_reflns_all 3330 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.00 _refine.ls_d_res_high 1.60 _refine.ls_percent_reflns_obs 99.9 _refine.ls_R_factor_obs 0.1828000 _refine.ls_R_factor_all 0.1835000 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.2287000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.8 _refine.ls_number_reflns_R_free 325 _refine.ls_number_parameters 843 _refine.ls_number_restraints 1426 _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _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 'BULK SOLVENT MODELING: MOEWS & KRETSINGER, J.MOL.BIOL. 91, 201-228 (1973)' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ? _refine.pdbx_starting_model '2.21A P 62 2 2 STRUCTURE OF H(GTGTACAC) (NDB CODE HD0002) WAS USED AS MODEL' _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case 'ALL OTHER CHEMICALLY EQUIVALENT BOND DISTANCES AND ANGLES WERE RESTRAINED TO BE SIMILAR BY SAME DISTANCE RESTRAINTS' _refine.pdbx_R_Free_selection_details RANDOM _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.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _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.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_analyze.entry_id 481D _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen 0. _refine_analyze.occupancy_sum_non_hydrogen 210. _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 169 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 40 _refine_hist.number_atoms_total 209 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 20.00 # 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 s_bond_d 0.013 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.019 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.046 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.026 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.011 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.031 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 481D _pdbx_refine.R_factor_all_no_cutoff 0.1840000 _pdbx_refine.R_factor_obs_no_cutoff 0.1830000 _pdbx_refine.free_R_factor_no_cutoff 0.2290000 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 9.8 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 325 _pdbx_refine.R_factor_all_4sig_cutoff 0.1735000 _pdbx_refine.R_factor_obs_4sig_cutoff 0.1729000 _pdbx_refine.free_R_factor_4sig_cutoff 0.2136000 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 9.9 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 297 _pdbx_refine.number_reflns_obs_4sig_cutoff 3011 _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 481D _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 481D _struct.title 'CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 481D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'HEXITOL NUCLEIC ACID, DNA ANALOGUE, DOUBLE HELIX, 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 481D _struct_ref.pdbx_db_accession 481D _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 481D _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 481D _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 # 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,x-y,-z 0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _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 covale1 covale both ? A 6HG 1 "O3'" ? ? ? 1_555 A 6HT 2 P ? ? A 6HG 1 A 6HT 2 1_555 ? ? ? ? ? ? ? 1.588 ? ? covale2 covale both ? A 6HT 2 "O3'" ? ? ? 1_555 A 6HG 3 P ? ? A 6HT 2 A 6HG 3 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale3 covale both ? A 6HG 3 "O3'" ? ? ? 1_555 A 6HT 4 P ? ? A 6HG 3 A 6HT 4 1_555 ? ? ? ? ? ? ? 1.581 ? ? covale4 covale both ? A 6HT 4 "O3'" ? ? ? 1_555 A 6HA 5 P ? ? A 6HT 4 A 6HA 5 1_555 ? ? ? ? ? ? ? 1.592 ? ? covale5 covale both ? A 6HA 5 "O3'" ? ? ? 1_555 A 6HC 6 P ? ? A 6HA 5 A 6HC 6 1_555 ? ? ? ? ? ? ? 1.592 ? ? covale6 covale both ? A 6HC 6 "O3'" ? ? ? 1_555 A 6HA 7 P ? ? A 6HC 6 A 6HA 7 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale7 covale both ? A 6HA 7 "O3'" ? ? ? 1_555 A 6HC 8 P ? ? A 6HA 7 A 6HC 8 1_555 ? ? ? ? ? ? ? 1.598 ? ? hydrog1 hydrog ? ? A 6HG 1 N1 ? ? ? 1_555 A 6HC 8 N3 ? ? A 6HG 1 A 6HC 8 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A 6HG 1 N2 ? ? ? 1_555 A 6HC 8 O2 ? ? A 6HG 1 A 6HC 8 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A 6HG 1 O6 ? ? ? 1_555 A 6HC 8 N4 ? ? A 6HG 1 A 6HC 8 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A 6HT 2 N3 ? ? ? 1_555 A 6HA 7 N1 ? ? A 6HT 2 A 6HA 7 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A 6HT 2 O4 ? ? ? 1_555 A 6HA 7 N6 ? ? A 6HT 2 A 6HA 7 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A 6HG 3 N1 ? ? ? 1_555 A 6HC 6 N3 ? ? A 6HG 3 A 6HC 6 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A 6HG 3 N2 ? ? ? 1_555 A 6HC 6 O2 ? ? A 6HG 3 A 6HC 6 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A 6HG 3 O6 ? ? ? 1_555 A 6HC 6 N4 ? ? A 6HG 3 A 6HC 6 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A 6HT 4 N3 ? ? ? 1_555 A 6HA 5 N1 ? ? A 6HT 4 A 6HA 5 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 6HT 4 O4 ? ? ? 1_555 A 6HA 5 N6 ? ? A 6HT 4 A 6HA 5 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A 6HA 5 N1 ? ? ? 1_555 A 6HT 4 N3 ? ? A 6HA 5 A 6HT 4 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A 6HA 5 N6 ? ? ? 1_555 A 6HT 4 O4 ? ? A 6HA 5 A 6HT 4 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A 6HC 6 N3 ? ? ? 1_555 A 6HG 3 N1 ? ? A 6HC 6 A 6HG 3 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 6HC 6 N4 ? ? ? 1_555 A 6HG 3 O6 ? ? A 6HC 6 A 6HG 3 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 6HC 6 O2 ? ? ? 1_555 A 6HG 3 N2 ? ? A 6HC 6 A 6HG 3 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A 6HA 7 N1 ? ? ? 1_555 A 6HT 2 N3 ? ? A 6HA 7 A 6HT 2 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A 6HA 7 N6 ? ? ? 1_555 A 6HT 2 O4 ? ? A 6HA 7 A 6HT 2 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A 6HC 8 N3 ? ? ? 1_555 A 6HG 1 N1 ? ? A 6HC 8 A 6HG 1 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A 6HC 8 N4 ? ? ? 1_555 A 6HG 1 O6 ? ? A 6HC 8 A 6HG 1 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A 6HC 8 O2 ? ? ? 1_555 A 6HG 1 N2 ? ? A 6HC 8 A 6HG 1 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 6HC _pdbx_validate_rmsd_angle.auth_seq_id_1 6 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 P _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 6HA _pdbx_validate_rmsd_angle.auth_seq_id_2 7 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OP2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 6HA _pdbx_validate_rmsd_angle.auth_seq_id_3 7 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 117.70 _pdbx_validate_rmsd_angle.angle_target_value 110.50 _pdbx_validate_rmsd_angle.angle_deviation 7.20 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.10 _pdbx_validate_rmsd_angle.linker_flag Y # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 6HG 1 A 6HG 1 ? DG ? 2 A 6HT 2 A 6HT 2 ? DT ? 3 A 6HG 3 A 6HG 3 ? DG ? 4 A 6HT 4 A 6HT 4 ? DT ? 5 A 6HA 5 A 6HA 5 ? DA ? 6 A 6HC 6 A 6HC 6 ? DC ? 7 A 6HA 7 A 6HA 7 ? DA ? 8 A 6HC 8 A 6HC 8 ? DC ? # 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 6HA P P N N 1 6HA OP1 O N N 2 6HA OP2 O N N 3 6HA OP3 O N N 4 6HA "O5'" O N N 5 6HA "C5'" C N N 6 6HA "C4'" C N R 7 6HA "O4'" O N N 8 6HA "C3'" C N S 9 6HA "O3'" O N N 10 6HA "C2'" C N N 11 6HA "C1'" C N S 12 6HA "C6'" C N N 13 6HA N9 N Y N 14 6HA C8 C Y N 15 6HA N7 N Y N 16 6HA C5 C Y N 17 6HA C6 C Y N 18 6HA N6 N N N 19 6HA N1 N Y N 20 6HA C2 C Y N 21 6HA N3 N Y N 22 6HA C4 C Y N 23 6HA HOP2 H N N 24 6HA HOP3 H N N 25 6HA "H5'" H N N 26 6HA "H5''" H N N 27 6HA "H4'" H N N 28 6HA "H3'" H N N 29 6HA "HO3'" H N N 30 6HA "H2'" H N N 31 6HA "H2''" H N N 32 6HA "H1'" H N N 33 6HA "H6'1" H N N 34 6HA "H6'2" H N N 35 6HA H8 H N N 36 6HA H61 H N N 37 6HA H62 H N N 38 6HA H2 H N N 39 6HC P P N N 40 6HC OP1 O N N 41 6HC OP2 O N N 42 6HC OP3 O N N 43 6HC "O5'" O N N 44 6HC "C5'" C N N 45 6HC "C4'" C N R 46 6HC "O4'" O N N 47 6HC "C3'" C N S 48 6HC "O3'" O N N 49 6HC "C2'" C N N 50 6HC "C1'" C N S 51 6HC "C6'" C N N 52 6HC N1 N N N 53 6HC C2 C N N 54 6HC O2 O N N 55 6HC N3 N N N 56 6HC C4 C N N 57 6HC N4 N N N 58 6HC C5 C N N 59 6HC C6 C N N 60 6HC HOP2 H N N 61 6HC HOP3 H N N 62 6HC "H5'" H N N 63 6HC "H5''" H N N 64 6HC "H4'" H N N 65 6HC "H3'" H N N 66 6HC "HO3'" H N N 67 6HC "H2'" H N N 68 6HC "H2''" H N N 69 6HC "H1'" H N N 70 6HC "H6'1" H N N 71 6HC "H6'2" H N N 72 6HC H41 H N N 73 6HC H42 H N N 74 6HC H5 H N N 75 6HC H6 H N N 76 6HG P P N N 77 6HG OP1 O N N 78 6HG OP2 O N N 79 6HG OP3 O N N 80 6HG "O5'" O N N 81 6HG "C5'" C N N 82 6HG "C4'" C N R 83 6HG "O4'" O N N 84 6HG "C3'" C N S 85 6HG "O3'" O N N 86 6HG "C2'" C N N 87 6HG "C1'" C N S 88 6HG "C6'" C N N 89 6HG N9 N Y N 90 6HG C8 C Y N 91 6HG N7 N Y N 92 6HG C5 C Y N 93 6HG C6 C N N 94 6HG O6 O N N 95 6HG N1 N N N 96 6HG C2 C N N 97 6HG N2 N N N 98 6HG N3 N N N 99 6HG C4 C Y N 100 6HG HOP2 H N N 101 6HG HOP3 H N N 102 6HG "H5'" H N N 103 6HG "H5''" H N N 104 6HG "H4'" H N N 105 6HG "H3'" H N N 106 6HG "HO3'" H N N 107 6HG "H2'" H N N 108 6HG "H2''" H N N 109 6HG "H1'" H N N 110 6HG "H6'1" H N N 111 6HG "H6'2" H N N 112 6HG H8 H N N 113 6HG H1 H N N 114 6HG H21 H N N 115 6HG H22 H N N 116 6HT P P N N 117 6HT OP1 O N N 118 6HT OP2 O N N 119 6HT OP3 O N N 120 6HT "O5'" O N N 121 6HT "C5'" C N N 122 6HT "C4'" C N R 123 6HT "O4'" O N N 124 6HT "C3'" C N S 125 6HT "O3'" O N N 126 6HT "C2'" C N N 127 6HT "C1'" C N S 128 6HT "C6'" C N N 129 6HT N1 N N N 130 6HT C2 C N N 131 6HT O2 O N N 132 6HT N3 N N N 133 6HT C4 C N N 134 6HT O4 O N N 135 6HT C5 C N N 136 6HT C5M C N N 137 6HT C6 C N N 138 6HT HOP2 H N N 139 6HT HOP3 H N N 140 6HT "H5'" H N N 141 6HT "H5''" H N N 142 6HT "H4'" H N N 143 6HT "H3'" H N N 144 6HT "HO3'" H N N 145 6HT "H2'" H N N 146 6HT "H2''" H N N 147 6HT "H1'" H N N 148 6HT "H6'1" H N N 149 6HT "H6'2" H N N 150 6HT H3 H N N 151 6HT H71 H N N 152 6HT H72 H N N 153 6HT H73 H N N 154 6HT H6 H N N 155 HOH O O N N 156 HOH H1 H N N 157 HOH H2 H N N 158 # 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 6HA P OP1 doub N N 1 6HA P OP2 sing N N 2 6HA P OP3 sing N N 3 6HA P "O5'" sing N N 4 6HA OP2 HOP2 sing N N 5 6HA OP3 HOP3 sing N N 6 6HA "O5'" "C5'" sing N N 7 6HA "C5'" "C4'" sing N N 8 6HA "C5'" "H5'" sing N N 9 6HA "C5'" "H5''" sing N N 10 6HA "C4'" "O4'" sing N N 11 6HA "C4'" "C3'" sing N N 12 6HA "C4'" "H4'" sing N N 13 6HA "O4'" "C6'" sing N N 14 6HA "C3'" "O3'" sing N N 15 6HA "C3'" "C2'" sing N N 16 6HA "C3'" "H3'" sing N N 17 6HA "O3'" "HO3'" sing N N 18 6HA "C2'" "C1'" sing N N 19 6HA "C2'" "H2'" sing N N 20 6HA "C2'" "H2''" sing N N 21 6HA "C1'" "C6'" sing N N 22 6HA "C1'" N9 sing N N 23 6HA "C1'" "H1'" sing N N 24 6HA "C6'" "H6'1" sing N N 25 6HA "C6'" "H6'2" sing N N 26 6HA N9 C8 sing Y N 27 6HA N9 C4 sing Y N 28 6HA C8 N7 doub Y N 29 6HA C8 H8 sing N N 30 6HA N7 C5 sing Y N 31 6HA C5 C6 sing Y N 32 6HA C5 C4 doub Y N 33 6HA C6 N6 sing N N 34 6HA C6 N1 doub Y N 35 6HA N6 H61 sing N N 36 6HA N6 H62 sing N N 37 6HA N1 C2 sing Y N 38 6HA C2 N3 doub Y N 39 6HA C2 H2 sing N N 40 6HA N3 C4 sing Y N 41 6HC P OP1 doub N N 42 6HC P OP2 sing N N 43 6HC P OP3 sing N N 44 6HC P "O5'" sing N N 45 6HC OP2 HOP2 sing N N 46 6HC OP3 HOP3 sing N N 47 6HC "O5'" "C5'" sing N N 48 6HC "C5'" "C4'" sing N N 49 6HC "C5'" "H5'" sing N N 50 6HC "C5'" "H5''" sing N N 51 6HC "C4'" "O4'" sing N N 52 6HC "C4'" "C3'" sing N N 53 6HC "C4'" "H4'" sing N N 54 6HC "O4'" "C6'" sing N N 55 6HC "C3'" "O3'" sing N N 56 6HC "C3'" "C2'" sing N N 57 6HC "C3'" "H3'" sing N N 58 6HC "O3'" "HO3'" sing N N 59 6HC "C2'" "C1'" sing N N 60 6HC "C2'" "H2'" sing N N 61 6HC "C2'" "H2''" sing N N 62 6HC "C1'" "C6'" sing N N 63 6HC "C1'" N1 sing N N 64 6HC "C1'" "H1'" sing N N 65 6HC "C6'" "H6'1" sing N N 66 6HC "C6'" "H6'2" sing N N 67 6HC N1 C2 sing N N 68 6HC N1 C6 sing N N 69 6HC C2 O2 doub N N 70 6HC C2 N3 sing N N 71 6HC N3 C4 doub N N 72 6HC C4 N4 sing N N 73 6HC C4 C5 sing N N 74 6HC N4 H41 sing N N 75 6HC N4 H42 sing N N 76 6HC C5 C6 doub N N 77 6HC C5 H5 sing N N 78 6HC C6 H6 sing N N 79 6HG P OP1 doub N N 80 6HG P OP2 sing N N 81 6HG P OP3 sing N N 82 6HG P "O5'" sing N N 83 6HG OP2 HOP2 sing N N 84 6HG OP3 HOP3 sing N N 85 6HG "O5'" "C5'" sing N N 86 6HG "C5'" "C4'" sing N N 87 6HG "C5'" "H5'" sing N N 88 6HG "C5'" "H5''" sing N N 89 6HG "C4'" "O4'" sing N N 90 6HG "C4'" "C3'" sing N N 91 6HG "C4'" "H4'" sing N N 92 6HG "O4'" "C6'" sing N N 93 6HG "C3'" "O3'" sing N N 94 6HG "C3'" "C2'" sing N N 95 6HG "C3'" "H3'" sing N N 96 6HG "O3'" "HO3'" sing N N 97 6HG "C2'" "C1'" sing N N 98 6HG "C2'" "H2'" sing N N 99 6HG "C2'" "H2''" sing N N 100 6HG "C1'" "C6'" sing N N 101 6HG "C1'" N9 sing N N 102 6HG "C1'" "H1'" sing N N 103 6HG "C6'" "H6'1" sing N N 104 6HG "C6'" "H6'2" sing N N 105 6HG N9 C8 sing Y N 106 6HG N9 C4 sing Y N 107 6HG C8 N7 doub Y N 108 6HG C8 H8 sing N N 109 6HG N7 C5 sing Y N 110 6HG C5 C6 sing N N 111 6HG C5 C4 doub Y N 112 6HG C6 O6 doub N N 113 6HG C6 N1 sing N N 114 6HG N1 C2 sing N N 115 6HG N1 H1 sing N N 116 6HG C2 N2 sing N N 117 6HG C2 N3 doub N N 118 6HG N2 H21 sing N N 119 6HG N2 H22 sing N N 120 6HG N3 C4 sing N N 121 6HT P OP1 doub N N 122 6HT P OP2 sing N N 123 6HT P OP3 sing N N 124 6HT P "O5'" sing N N 125 6HT OP2 HOP2 sing N N 126 6HT OP3 HOP3 sing N N 127 6HT "O5'" "C5'" sing N N 128 6HT "C5'" "C4'" sing N N 129 6HT "C5'" "H5'" sing N N 130 6HT "C5'" "H5''" sing N N 131 6HT "C4'" "O4'" sing N N 132 6HT "C4'" "C3'" sing N N 133 6HT "C4'" "H4'" sing N N 134 6HT "O4'" "C6'" sing N N 135 6HT "C3'" "O3'" sing N N 136 6HT "C3'" "C2'" sing N N 137 6HT "C3'" "H3'" sing N N 138 6HT "O3'" "HO3'" sing N N 139 6HT "C2'" "C1'" sing N N 140 6HT "C2'" "H2'" sing N N 141 6HT "C2'" "H2''" sing N N 142 6HT "C1'" "C6'" sing N N 143 6HT "C1'" N1 sing N N 144 6HT "C1'" "H1'" sing N N 145 6HT "C6'" "H6'1" sing N N 146 6HT "C6'" "H6'2" sing N N 147 6HT N1 C2 sing N N 148 6HT N1 C6 sing N N 149 6HT C2 O2 doub N N 150 6HT C2 N3 sing N N 151 6HT N3 C4 sing N N 152 6HT N3 H3 sing N N 153 6HT C4 O4 doub N N 154 6HT C4 C5 sing N N 155 6HT C5 C5M sing N N 156 6HT C5 C6 doub N N 157 6HT C5M H71 sing N N 158 6HT C5M H72 sing N N 159 6HT C5M H73 sing N N 160 6HT C6 H6 sing N N 161 HOH O H1 sing N N 162 HOH O H2 sing N N 163 # _ndb_struct_conf_na.entry_id 481D _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 6HG 1 1_555 A 6HC 8 6_555 -0.254 -0.212 -0.393 -12.443 16.520 -0.282 1 A_6HG1:6HC8_A A 1 ? A 8 ? 19 1 1 A 6HT 2 1_555 A 6HA 7 6_555 0.035 -0.099 -0.015 -0.558 7.128 0.900 2 A_6HT2:6HA7_A A 2 ? A 7 ? 20 1 1 A 6HG 3 1_555 A 6HC 6 6_555 -0.241 -0.175 0.100 3.903 1.571 -1.700 3 A_6HG3:6HC6_A A 3 ? A 6 ? 19 1 1 A 6HT 4 1_555 A 6HA 5 6_555 -0.023 -0.123 -0.113 2.447 -0.785 0.885 4 A_6HT4:6HA5_A A 4 ? A 5 ? 20 1 1 A 6HA 5 1_555 A 6HT 4 6_555 0.023 -0.123 -0.113 -2.447 -0.785 0.885 5 A_6HA5:6HT4_A A 5 ? A 4 ? 20 1 1 A 6HC 6 1_555 A 6HG 3 6_555 0.241 -0.175 0.100 -3.903 1.571 -1.700 6 A_6HC6:6HG3_A A 6 ? A 3 ? 19 1 1 A 6HA 7 1_555 A 6HT 2 6_555 -0.035 -0.099 -0.015 0.558 7.128 0.900 7 A_6HA7:6HT2_A A 7 ? A 2 ? 20 1 1 A 6HC 8 1_555 A 6HG 1 6_555 0.254 -0.212 -0.393 12.443 16.520 -0.282 8 A_6HC8:6HG1_A A 8 ? A 1 ? 19 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 6HG 1 1_555 A 6HC 8 6_555 A 6HT 2 1_555 A 6HA 7 6_555 -0.237 -2.851 3.272 -0.390 4.004 25.617 -7.388 0.428 2.804 8.959 0.873 25.925 1 AA_6HG16HT2:6HA76HC8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A 6HT 2 1_555 A 6HA 7 6_555 A 6HG 3 1_555 A 6HC 6 6_555 -0.020 -2.018 3.214 -1.357 1.457 27.269 -4.619 -0.284 3.102 3.085 2.873 27.340 2 AA_6HT26HG3:6HC66HA7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A 6HG 3 1_555 A 6HC 6 6_555 A 6HT 4 1_555 A 6HA 5 6_555 0.560 -2.899 3.294 2.304 4.103 29.900 -6.346 -0.628 2.914 7.890 -4.432 30.260 3 AA_6HG36HT4:6HA56HC6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A 6HT 4 1_555 A 6HA 5 6_555 A 6HA 5 1_555 A 6HT 4 6_555 0.000 -4.203 3.442 0.000 6.800 15.714 -17.544 0.000 1.503 23.489 0.000 17.114 4 AA_6HT46HA5:6HT46HA5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A 6HA 5 1_555 A 6HT 4 6_555 A 6HC 6 1_555 A 6HG 3 6_555 -0.560 -2.899 3.294 -2.305 4.103 29.900 -6.346 0.628 2.914 7.890 4.432 30.260 5 AA_6HA56HC6:6HG36HT4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A 6HC 6 1_555 A 6HG 3 6_555 A 6HA 7 1_555 A 6HT 2 6_555 0.020 -2.018 3.214 1.357 1.457 27.269 -4.619 0.284 3.102 3.085 -2.873 27.340 6 AA_6HC66HA7:6HT26HG3_AA A 6 ? A 3 ? A 7 ? A 2 ? 1 A 6HA 7 1_555 A 6HT 2 6_555 A 6HC 8 1_555 A 6HG 1 6_555 0.237 -2.851 3.272 0.390 4.004 25.617 -7.388 -0.428 2.804 8.959 -0.873 25.925 7 AA_6HA76HC8:6HG16HT2_AA A 7 ? A 2 ? A 8 ? A 1 ? # _pdbx_initial_refinement_model.accession_code 1D7Z _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 '2.21A P 62 2 2 STRUCTURE OF H(GTGTACAC) (NDB CODE HD0002) WAS USED AS MODEL' # _atom_sites.entry_id 481D _atom_sites.fract_transf_matrix[1][1] 0.030265 _atom_sites.fract_transf_matrix[1][2] 0.017474 _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] 0.034948 _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] 0.025691 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P # loop_