data_2KWG # _entry.id 2KWG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2KWG RCSB RCSB101658 WWPDB D_1000101658 # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KWG _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-04-09 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Podbevsek, P.' 1 'Bhat, B.' 2 'Plavec, J.' 3 # _citation.id primary _citation.title ;Solution-state structure of a fully alternately 2'-F/2'-OMe modified 42-nt dimeric siRNA construct. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 38 _citation.page_first 7298 _citation.page_last 7307 _citation.year 2010 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20624819 _citation.pdbx_database_id_DOI 10.1093/nar/gkq621 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Podbevsek, P.' 1 primary 'Allerson, C.R.' 2 primary 'Bhat, B.' 3 primary 'Plavec, J.' 4 # _cell.entry_id 2KWG _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 2KWG _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 ;5'-R(*(GF2)P*(OMG)P*(GF2)P*(OMU)P*(AF2)P*(A2M)P*(AF2)P*(OMU)P*(AF2)P*(OMC)P*(AF2)P*(OMU)P*(UFT)P*(OMC)P*(UFT)P*(OMU)P*(CFZ)P*(A2M)P*(UFT)P*(OMU)P*(UFT))-3' ; 6799.100 1 ? ? ? ? 2 polymer syn ;5'-R(P*(A2M)P*(UFT)P*(OMG)P*(AF2)P*(A2M)P*(GF2)P*(A2M)P*(AF2)P*(OMU)P*(GF2)P*(OMU)P*(AF2)P*(OMU)P*(UFT)P*(OMU)P*(AF2)P*(OMC)P*(CFZ)P*(OMC)P*(UFT)P*(OMU))-3' ; 6834.176 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes ;(GF2)(OMG)(GF2)(OMU)(AF2)(A2M)(AF2)(OMU)(AF2)(OMC)(AF2)(OMU)(UFT)(OMC)(UFT)(OMU) (CFZ)(A2M)(UFT)(OMU)(UFT) ; XGXUXAXUXCXUUCUUXAUUU A ? 2 polyribonucleotide no yes ;(A2M)(UFT)(OMG)(AF2)(A2M)(GF2)(A2M)(AF2)(OMU)(GF2)(OMU)(AF2)(OMU)(UFT)(OMU)(AF2) (OMC)(CFZ)(OMC)(UFT)(OMU) ; AUGXAXAXUXUXUUUXCXCUU B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GF2 n 1 2 OMG n 1 3 GF2 n 1 4 OMU n 1 5 AF2 n 1 6 A2M n 1 7 AF2 n 1 8 OMU n 1 9 AF2 n 1 10 OMC n 1 11 AF2 n 1 12 OMU n 1 13 UFT n 1 14 OMC n 1 15 UFT n 1 16 OMU n 1 17 CFZ n 1 18 A2M n 1 19 UFT n 1 20 OMU n 1 21 UFT n 2 1 A2M n 2 2 UFT n 2 3 OMG n 2 4 AF2 n 2 5 A2M n 2 6 GF2 n 2 7 A2M n 2 8 AF2 n 2 9 OMU n 2 10 GF2 n 2 11 OMU n 2 12 AF2 n 2 13 OMU n 2 14 UFT n 2 15 OMU n 2 16 AF2 n 2 17 OMC n 2 18 CFZ n 2 19 OMC n 2 20 UFT n 2 21 OMU n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2KWG 2KWG 1 ? ? ? 2 PDB 2KWG 2KWG 2 ? ? ? # 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 2KWG A 1 ? 21 ? 2KWG 1 ? 21 ? 1 21 2 2 2KWG B 1 ? 21 ? 2KWG 22 ? 42 ? 22 42 # 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 A2M 'RNA linking' n ;2'-O-methyladenosine 5'-(dihydrogen phosphate) ; ? 'C11 H16 N5 O7 P' 361.248 AF2 'DNA linking' n ;2'-deoxy-2'-fluoroadenosine 5'-(dihydrogen phosphate) ; ? 'C10 H13 F N5 O6 P' 349.212 CFZ 'DNA linking' n ;2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate) ; ? 'C9 H13 F N3 O7 P' 325.188 GF2 'DNA linking' n ;2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate) ; ? 'C10 H13 F N5 O7 P' 365.212 OMC 'RNA linking' n "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 OMG 'RNA linking' n "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O8 P' 377.247 OMU 'RNA linking' n ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O9 P' 338.208 UFT 'DNA linking' n ;2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate) ; ? 'C9 H12 F N2 O8 P' 326.172 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D DQF-COSY' 1 2 1 '2D 1H-1H NOESY' 1 3 2 '2D 1H-1H NOESY' 2 4 1 '2D 1H-1H NOESY' 2 5 2 '2D 1H-1H NOESY' 1 6 1 '2D HP-COSY' 1 7 1 '2D 1H-1H NOESY' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 20 6.8 ambient ? 25 K 2 20 6.8 ambient ? 5 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '2 mM RNA-1, 2 mM RNA-2, 100% D2O' 1 '100% D2O' '2 mM RNA-1, 2 mM RNA-2, 95% H2O/5% D2O' 2 '95% H2O/5% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 800 Varian 'Uniform NMR System' 1 'Varian Uniform NMR System' 600 Varian 'Uniform NMR System' 2 'Varian Uniform NMR System' # _pdbx_nmr_refine.entry_id 2KWG _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details '100 ps of NMR restrained simulated annealing calculations using a generalized Born implicit solvation model.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KWG _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2KWG _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal Goddard 'chemical shift assignment' SPARKY 3.115 1 Varian collection VNMRJ 2.2C 2 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' 'structure solution' AMBER 9 3 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' refinement AMBER 9 4 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KWG _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KWG _struct.title ;Solution structure of a fully modified 2'-F/2'-OMe siRNA construct ; _struct.pdbx_descriptor ;5'-R(*(GF2)P*(OMG)P*(GF2)P*(OMU)P*(AF2)P*(A2M)P*(AF2)P*(OMU)P*(AF2)P*(OMC)P*(AF2)P*(OMU)P*(UFT)P*(OMC)P*(UFT)P*(OMU)P*(CFZ)P*(A2M)P*(UFT)P*(OMU)P*(UFT))-3'/5'-R(P*(A2M)P*(UFT)P*(OMG)P*(AF2)P*(A2M)P*(GF2)P*(A2M)P*(AF2)P*(OMU)P*(GF2)P*(OMU)P*(AF2)P*(OMU)P*(UFT)P*(OMU)P*(AF2)P*(OMC)P*(CFZ)P*(OMC)P*(UFT)P*(OMU))-3' ; _struct.pdbx_model_details 'lowest energy, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KWG _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;siRNA, 2'-fluoro, 2'-O-methyl, RNA ; # 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_biol.id 1 _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 covale1 covale ? ? A OMG 2 "O3'" ? ? ? 1_555 A GF2 3 P ? ? A OMG 2 A GF2 3 1_555 ? ? ? ? ? ? ? 1.610 ? covale2 covale ? ? A OMU 4 "O3'" ? ? ? 1_555 A AF2 5 P ? ? A OMU 4 A AF2 5 1_555 ? ? ? ? ? ? ? 1.611 ? covale3 covale ? ? A A2M 6 "O3'" ? ? ? 1_555 A AF2 7 P ? ? A A2M 6 A AF2 7 1_555 ? ? ? ? ? ? ? 1.611 ? covale4 covale ? ? A OMU 8 "O3'" ? ? ? 1_555 A AF2 9 P ? ? A OMU 8 A AF2 9 1_555 ? ? ? ? ? ? ? 1.611 ? covale5 covale ? ? A OMC 10 "O3'" ? ? ? 1_555 A AF2 11 P ? ? A OMC 10 A AF2 11 1_555 ? ? ? ? ? ? ? 1.612 ? covale6 covale ? ? A OMU 12 "O3'" ? ? ? 1_555 A UFT 13 P ? ? A OMU 12 A UFT 13 1_555 ? ? ? ? ? ? ? 1.611 ? covale7 covale ? ? A UFT 13 "O3'" ? ? ? 1_555 A OMC 14 P ? ? A UFT 13 A OMC 14 1_555 ? ? ? ? ? ? ? 1.600 ? covale8 covale ? ? A OMC 14 "O3'" ? ? ? 1_555 A UFT 15 P ? ? A OMC 14 A UFT 15 1_555 ? ? ? ? ? ? ? 1.608 ? covale9 covale ? ? A UFT 15 "O3'" ? ? ? 1_555 A OMU 16 P ? ? A UFT 15 A OMU 16 1_555 ? ? ? ? ? ? ? 1.603 ? covale10 covale ? ? A OMU 16 "O3'" ? ? ? 1_555 A CFZ 17 P ? ? A OMU 16 A CFZ 17 1_555 ? ? ? ? ? ? ? 1.610 ? covale11 covale ? ? A CFZ 17 "O3'" ? ? ? 1_555 A A2M 18 P ? ? A CFZ 17 A A2M 18 1_555 ? ? ? ? ? ? ? 1.600 ? covale12 covale ? ? A A2M 18 "O3'" ? ? ? 1_555 A UFT 19 P ? ? A A2M 18 A UFT 19 1_555 ? ? ? ? ? ? ? 1.611 ? covale13 covale ? ? A UFT 19 "O3'" ? ? ? 1_555 A OMU 20 P ? ? A UFT 19 A OMU 20 1_555 ? ? ? ? ? ? ? 1.598 ? covale14 covale ? ? A OMU 20 "O3'" ? ? ? 1_555 A UFT 21 P ? ? A OMU 20 A UFT 21 1_555 ? ? ? ? ? ? ? 1.610 ? covale15 covale ? ? B A2M 1 "O3'" ? ? ? 1_555 B UFT 2 P ? ? B A2M 22 B UFT 23 1_555 ? ? ? ? ? ? ? 1.610 ? covale16 covale ? ? B UFT 2 "O3'" ? ? ? 1_555 B OMG 3 P ? ? B UFT 23 B OMG 24 1_555 ? ? ? ? ? ? ? 1.599 ? covale17 covale ? ? B OMG 3 "O3'" ? ? ? 1_555 B AF2 4 P ? ? B OMG 24 B AF2 25 1_555 ? ? ? ? ? ? ? 1.608 ? covale18 covale ? ? B A2M 5 "O3'" ? ? ? 1_555 B GF2 6 P ? ? B A2M 26 B GF2 27 1_555 ? ? ? ? ? ? ? 1.611 ? covale19 covale ? ? B A2M 7 "O3'" ? ? ? 1_555 B AF2 8 P ? ? B A2M 28 B AF2 29 1_555 ? ? ? ? ? ? ? 1.611 ? covale20 covale ? ? B OMU 9 "O3'" ? ? ? 1_555 B GF2 10 P ? ? B OMU 30 B GF2 31 1_555 ? ? ? ? ? ? ? 1.612 ? covale21 covale ? ? B OMU 11 "O3'" ? ? ? 1_555 B AF2 12 P ? ? B OMU 32 B AF2 33 1_555 ? ? ? ? ? ? ? 1.611 ? covale22 covale ? ? B OMU 13 "O3'" ? ? ? 1_555 B UFT 14 P ? ? B OMU 34 B UFT 35 1_555 ? ? ? ? ? ? ? 1.608 ? covale23 covale ? ? B UFT 14 "O3'" ? ? ? 1_555 B OMU 15 P ? ? B UFT 35 B OMU 36 1_555 ? ? ? ? ? ? ? 1.601 ? covale24 covale ? ? B OMU 15 "O3'" ? ? ? 1_555 B AF2 16 P ? ? B OMU 36 B AF2 37 1_555 ? ? ? ? ? ? ? 1.609 ? covale25 covale ? ? B OMC 17 "O3'" ? ? ? 1_555 B CFZ 18 P ? ? B OMC 38 B CFZ 39 1_555 ? ? ? ? ? ? ? 1.610 ? covale26 covale ? ? B CFZ 18 "O3'" ? ? ? 1_555 B OMC 19 P ? ? B CFZ 39 B OMC 40 1_555 ? ? ? ? ? ? ? 1.609 ? covale27 covale ? ? B OMC 19 "O3'" ? ? ? 1_555 B UFT 20 P ? ? B OMC 40 B UFT 41 1_555 ? ? ? ? ? ? ? 1.613 ? covale28 covale ? ? B UFT 20 "O3'" ? ? ? 1_555 B OMU 21 P ? ? B UFT 41 B OMU 42 1_555 ? ? ? ? ? ? ? 1.596 ? hydrog1 hydrog ? ? A A2M 6 N1 ? ? ? 1_555 B UFT 14 N3 ? ? A A2M 6 B UFT 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A A2M 6 N6 ? ? ? 1_555 B UFT 14 O4 ? ? A A2M 6 B UFT 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A UFT 13 N3 ? ? ? 1_555 B A2M 7 N1 ? ? A UFT 13 B A2M 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A UFT 13 O4 ? ? ? 1_555 B A2M 7 N6 ? ? A UFT 13 B A2M 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A UFT 15 N3 ? ? ? 1_555 B A2M 5 N1 ? ? A UFT 15 B A2M 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A UFT 15 O4 ? ? ? 1_555 B A2M 5 N6 ? ? A UFT 15 B A2M 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A A2M 18 N1 ? ? ? 1_555 B UFT 2 N3 ? ? A A2M 18 B UFT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A A2M 18 N6 ? ? ? 1_555 B UFT 2 O4 ? ? A A2M 18 B UFT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A UFT 19 N3 ? ? ? 1_555 B A2M 1 N1 ? ? A UFT 19 B A2M 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A UFT 19 O4 ? ? ? 1_555 B A2M 1 N6 ? ? A UFT 19 B A2M 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2KWG _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 F H 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 GF2 1 1 1 GF2 GF2 A . n A 1 2 OMG 2 2 2 OMG OMG A . n A 1 3 GF2 3 3 3 GF2 GF2 A . n A 1 4 OMU 4 4 4 OMU OMU A . n A 1 5 AF2 5 5 5 AF2 AF2 A . n A 1 6 A2M 6 6 6 A2M A2M A . n A 1 7 AF2 7 7 7 AF2 AF2 A . n A 1 8 OMU 8 8 8 OMU OMU A . n A 1 9 AF2 9 9 9 AF2 AF2 A . n A 1 10 OMC 10 10 10 OMC OMC A . n A 1 11 AF2 11 11 11 AF2 AF2 A . n A 1 12 OMU 12 12 12 OMU OMU A . n A 1 13 UFT 13 13 13 UFT UFT A . n A 1 14 OMC 14 14 14 OMC OMC A . n A 1 15 UFT 15 15 15 UFT UFT A . n A 1 16 OMU 16 16 16 OMU OMU A . n A 1 17 CFZ 17 17 17 CFZ CFZ A . n A 1 18 A2M 18 18 18 A2M A2M A . n A 1 19 UFT 19 19 19 UFT UFT A . n A 1 20 OMU 20 20 20 OMU OMU A . n A 1 21 UFT 21 21 21 UFT UFT A . n B 2 1 A2M 1 22 22 A2M A2M B . n B 2 2 UFT 2 23 23 UFT UFT B . n B 2 3 OMG 3 24 24 OMG OMG B . n B 2 4 AF2 4 25 25 AF2 AF2 B . n B 2 5 A2M 5 26 26 A2M A2M B . n B 2 6 GF2 6 27 27 GF2 GF2 B . n B 2 7 A2M 7 28 28 A2M A2M B . n B 2 8 AF2 8 29 29 AF2 AF2 B . n B 2 9 OMU 9 30 30 OMU OMU B . n B 2 10 GF2 10 31 31 GF2 GF2 B . n B 2 11 OMU 11 32 32 OMU OMU B . n B 2 12 AF2 12 33 33 AF2 AF2 B . n B 2 13 OMU 13 34 34 OMU OMU B . n B 2 14 UFT 14 35 35 UFT UFT B . n B 2 15 OMU 15 36 36 OMU OMU B . n B 2 16 AF2 16 37 37 AF2 AF2 B . n B 2 17 OMC 17 38 38 OMC OMC B . n B 2 18 CFZ 18 39 39 CFZ CFZ B . n B 2 19 OMC 19 40 40 OMC OMC B . n B 2 20 UFT 20 41 41 UFT UFT B . n B 2 21 OMU 21 42 42 OMU OMU B . n # 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 GF2 1 A GF2 1 ? DG ? 2 A OMG 2 A OMG 2 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 3 A GF2 3 A GF2 3 ? DG ? 4 A OMU 4 A OMU 4 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 5 A AF2 5 A AF2 5 ? DA ? 6 A A2M 6 A A2M 6 ? A ? 7 A AF2 7 A AF2 7 ? DA ? 8 A OMU 8 A OMU 8 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 9 A AF2 9 A AF2 9 ? DA ? 10 A OMC 10 A OMC 10 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 11 A AF2 11 A AF2 11 ? DA ? 12 A OMU 12 A OMU 12 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 13 A UFT 13 A UFT 13 ? DU ? 14 A OMC 14 A OMC 14 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 15 A UFT 15 A UFT 15 ? DU ? 16 A OMU 16 A OMU 16 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 17 A CFZ 17 A CFZ 17 ? DC ? 18 A A2M 18 A A2M 18 ? A ? 19 A UFT 19 A UFT 19 ? DU ? 20 A OMU 20 A OMU 20 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 21 A UFT 21 A UFT 21 ? DU ? 22 B A2M 1 B A2M 22 ? A ? 23 B UFT 2 B UFT 23 ? DU ? 24 B OMG 3 B OMG 24 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 25 B AF2 4 B AF2 25 ? DA ? 26 B A2M 5 B A2M 26 ? A ? 27 B GF2 6 B GF2 27 ? DG ? 28 B A2M 7 B A2M 28 ? A ? 29 B AF2 8 B AF2 29 ? DA ? 30 B OMU 9 B OMU 30 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 31 B GF2 10 B GF2 31 ? DG ? 32 B OMU 11 B OMU 32 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 33 B AF2 12 B AF2 33 ? DA ? 34 B OMU 13 B OMU 34 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 35 B UFT 14 B UFT 35 ? DU ? 36 B OMU 15 B OMU 36 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 37 B AF2 16 B AF2 37 ? DA ? 38 B OMC 17 B OMC 38 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 39 B CFZ 18 B CFZ 39 ? DC ? 40 B OMC 19 B OMC 40 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 41 B UFT 20 B UFT 41 ? DU ? 42 B OMU 21 B OMU 42 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; # _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 # _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_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 2010-07-21 2 'Structure model' 1 1 2011-07-13 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id ISIS401156-1 2 ? mM ? 1 ISIS401157-2 2 ? mM ? 1 ISIS401156-3 2 ? mM ? 2 ISIS401157-4 2 ? mM ? 2 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2KWG _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count 33 _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count 33 _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count 42 _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count 42 _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count 33 _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count 67 _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total ? _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 10 _pdbx_validate_close_contact.auth_atom_id_1 "HO5'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 GF2 _pdbx_validate_close_contact.auth_seq_id_1 1 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OP2 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 OMG _pdbx_validate_close_contact.auth_seq_id_2 2 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.48 # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 "C4'" ? B A2M 22 ? 'WRONG HAND' . 2 1 "C3'" ? B A2M 22 ? 'WRONG HAND' . 3 2 "C4'" ? B UFT 23 ? 'WRONG HAND' . 4 3 "C4'" ? B A2M 22 ? 'WRONG HAND' . 5 3 "C3'" ? B A2M 22 ? 'WRONG HAND' . 6 4 "C4'" ? B A2M 22 ? 'WRONG HAND' . 7 5 "C4'" ? B A2M 22 ? 'WRONG HAND' . 8 5 "C3'" ? B A2M 22 ? 'WRONG HAND' . 9 5 "C4'" ? B UFT 23 ? 'WRONG HAND' . 10 6 "C3'" ? B A2M 22 ? 'WRONG HAND' . 11 8 "C4'" ? B A2M 22 ? 'WRONG HAND' . 12 8 "C3'" ? B A2M 22 ? 'WRONG HAND' . 13 9 "C4'" ? B A2M 22 ? 'WRONG HAND' . 14 9 "C3'" ? B A2M 22 ? 'WRONG HAND' . 15 10 "C4'" ? B A2M 22 ? 'WRONG HAND' . 16 10 "C3'" ? B A2M 22 ? 'WRONG HAND' . # _ndb_struct_conf_na.entry_id 2KWG _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 A2M 6 1_555 B UFT 14 1_555 0.089 0.009 0.022 3.244 -6.890 -1.345 1 A_A2M6:UFT35_B A 6 ? B 35 ? 20 1 1 A UFT 13 1_555 B A2M 7 1_555 -0.087 -0.009 0.061 2.866 -6.147 -0.324 2 A_UFT13:A2M28_B A 13 ? B 28 ? 20 1 1 A UFT 15 1_555 B A2M 5 1_555 -0.067 0.034 -0.015 6.196 4.106 -4.280 3 A_UFT15:A2M26_B A 15 ? B 26 ? 20 1 1 A A2M 18 1_555 B UFT 2 1_555 0.222 0.049 0.150 16.562 -7.109 -2.132 4 A_A2M18:UFT23_B A 18 ? B 23 ? 20 1 1 A UFT 19 1_555 B A2M 1 1_555 0.048 -0.025 -0.565 14.423 -12.735 2.864 5 A_UFT19:A2M22_B A 19 ? B 22 ? 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 A2M _ndb_struct_na_base_pair_step.i_label_seq_id_1 18 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 B _ndb_struct_na_base_pair_step.j_label_comp_id_1 UFT _ndb_struct_na_base_pair_step.j_label_seq_id_1 2 _ndb_struct_na_base_pair_step.j_symmetry_1 1_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 UFT _ndb_struct_na_base_pair_step.i_label_seq_id_2 19 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 B _ndb_struct_na_base_pair_step.j_label_comp_id_2 A2M _ndb_struct_na_base_pair_step.j_label_seq_id_2 1 _ndb_struct_na_base_pair_step.j_symmetry_2 1_555 _ndb_struct_na_base_pair_step.shift 0.506 _ndb_struct_na_base_pair_step.slide -2.583 _ndb_struct_na_base_pair_step.rise 3.343 _ndb_struct_na_base_pair_step.tilt 1.755 _ndb_struct_na_base_pair_step.roll 7.027 _ndb_struct_na_base_pair_step.twist 25.762 _ndb_struct_na_base_pair_step.x_displacement -7.270 _ndb_struct_na_base_pair_step.y_displacement -0.672 _ndb_struct_na_base_pair_step.helical_rise 2.588 _ndb_struct_na_base_pair_step.inclination 15.378 _ndb_struct_na_base_pair_step.tip -3.841 _ndb_struct_na_base_pair_step.helical_twist 26.745 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_A2M18UFT19:A2M22UFT23_BB _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 18 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 B _ndb_struct_na_base_pair_step.j_auth_seq_id_1 23 _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 19 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 B _ndb_struct_na_base_pair_step.j_auth_seq_id_2 22 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? #