data_1XV6 # _entry.id 1XV6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 1XV6 pdb_00001xv6 10.2210/pdb1xv6/pdb RCSB RCSB030800 ? ? WWPDB D_1000030800 ? ? # 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 2005-04-05 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 5 'Structure model' 1 4 2024-05-29 # _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' Advisory 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Data collection' # 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' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 4 'Structure model' pdbx_validate_polymer_linkage 6 4 'Structure model' struct_conn 7 5 'Structure model' chem_comp_atom 8 5 'Structure model' chem_comp_bond # 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_nmr_software.name' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1XV6 _pdbx_database_status.recvd_initial_deposition_date 2004-10-27 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Plevnik, M.' 1 'Gdaniec, Z.' 2 'Plavec, J.' 3 # _citation.id primary _citation.title ;Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 33 _citation.page_first 1749 _citation.page_last 1759 _citation.year 2005 _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 15788747 _citation.pdbx_database_id_DOI 10.1093/nar/gki318 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Plevnik, M.' 1 ? primary 'Gdaniec, Z.' 2 ? primary 'Plavec, J.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-R(*(C2L)P*(G2L)P*(C2L)P*(G2L)P*(A2L)P*(A2L)P*(U2L)P*(U2L)P*(C2L)P*(G2L)P*(C2L)P*(G2L))-2'" _entity.formula_weight 4608.442 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name ;2'-MOE RNA ; # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(C2L)(G2L)(C2L)(G2L)(A2L)(A2L)(U2L)(U2L)(C2L)(G2L)(C2L)(G2L)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAAUUCGCG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C2L n 1 2 G2L n 1 3 C2L n 1 4 G2L n 1 5 A2L n 1 6 A2L n 1 7 U2L n 1 8 U2L n 1 9 C2L n 1 10 G2L n 1 11 C2L n 1 12 G2L n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'solid phase synthesis, phosphoramidite chemistry' # 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 A2L 'RNA linking' n ;3'-O-METHYOXYETHYL-ADENOSINE 5'-MONOPHOSPHATE ; ? 'C13 H20 N5 O8 P' 405.300 C2L 'RNA linking' n ;5-METHYL-3'-O-METHOXYETHYL CYTIDINE 5'-MONOPHOSPHATE ; ? 'C13 H22 N3 O9 P' 395.302 G2L 'RNA linking' n "3'-O-METHYOXYETHYL-GUANOSINE-5'-MONOPHOSPHATE" ? 'C13 H20 N5 O9 P' 421.300 U2L 'RNA linking' n ;5-METHYL-3'-O-METHOXYETHYL URIDINE-5'-MONOPHOSPHATE ; ? 'C13 H21 N2 O10 P' 396.287 # 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 C2L 1 1 1 C2L C2L A . n A 1 2 G2L 2 2 2 G2L G2L A . n A 1 3 C2L 3 3 3 C2L C2L A . n A 1 4 G2L 4 4 4 G2L G2L A . n A 1 5 A2L 5 5 5 A2L A2L A . n A 1 6 A2L 6 6 6 A2L A2L A . n A 1 7 U2L 7 7 7 U2L U2L A . n A 1 8 U2L 8 8 8 U2L U2L A . n A 1 9 C2L 9 9 9 C2L C2L A . n A 1 10 G2L 10 10 10 G2L G2L A . n A 1 11 C2L 11 11 11 C2L C2L A . n A 1 12 G2L 12 12 12 G2L G2L A . n # _exptl.entry_id 1XV6 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _database_PDB_matrix.entry_id 1XV6 _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 1XV6 _struct.title ;The solution structure of 2',5'-linked 3'-O-(2-methoxyethyl)-RNA hairpin ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1XV6 _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;hairpin, (2', 5')-RNA, 3'-O-(2-methoxyethyl) ribose, RNA ; # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1XV6 _struct_ref.pdbx_db_accession 1XV6 _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 1XV6 _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1XV6 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _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 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A C2L 1 "O2'" ? ? ? 1_555 A G2L 2 P ? ? A C2L 1 A G2L 2 1_555 ? ? ? ? ? ? ? 1.627 ? ? covale2 covale one ? A G2L 2 "O2'" ? ? ? 1_555 A C2L 3 P ? ? A G2L 2 A C2L 3 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale3 covale one ? A C2L 3 "O2'" ? ? ? 1_555 A G2L 4 P ? ? A C2L 3 A G2L 4 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale4 covale one ? A G2L 4 "O2'" ? ? ? 1_555 A A2L 5 P ? ? A G2L 4 A A2L 5 1_555 ? ? ? ? ? ? ? 1.632 ? ? covale5 covale one ? A A2L 5 "O2'" ? ? ? 1_555 A A2L 6 P ? ? A A2L 5 A A2L 6 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale6 covale one ? A A2L 6 "O2'" ? ? ? 1_555 A U2L 7 P ? ? A A2L 6 A U2L 7 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale7 covale one ? A U2L 7 "O2'" ? ? ? 1_555 A U2L 8 P ? ? A U2L 7 A U2L 8 1_555 ? ? ? ? ? ? ? 1.646 ? ? covale8 covale one ? A U2L 8 "O2'" ? ? ? 1_555 A C2L 9 P ? ? A U2L 8 A C2L 9 1_555 ? ? ? ? ? ? ? 1.624 ? ? covale9 covale one ? A C2L 9 "O2'" ? ? ? 1_555 A G2L 10 P ? ? A C2L 9 A G2L 10 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale10 covale one ? A G2L 10 "O2'" ? ? ? 1_555 A C2L 11 P ? ? A G2L 10 A C2L 11 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale11 covale one ? A C2L 11 "O2'" ? ? ? 1_555 A G2L 12 P ? ? A C2L 11 A G2L 12 1_555 ? ? ? ? ? ? ? 1.611 ? ? hydrog1 hydrog ? ? A C2L 1 N4 ? ? ? 1_555 A G2L 12 N3 ? ? A C2L 1 A G2L 12 1_555 ? ? ? ? ? ? 'C2L-G2L PAIR' ? ? ? hydrog2 hydrog ? ? A G2L 2 N1 ? ? ? 1_555 A C2L 11 N3 ? ? A G2L 2 A C2L 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G2L 2 N2 ? ? ? 1_555 A C2L 11 O2 ? ? A G2L 2 A C2L 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G2L 2 O6 ? ? ? 1_555 A C2L 11 N4 ? ? A G2L 2 A C2L 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C2L 3 N3 ? ? ? 1_555 A G2L 10 N1 ? ? A C2L 3 A G2L 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C2L 3 N4 ? ? ? 1_555 A G2L 10 O6 ? ? A C2L 3 A G2L 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C2L 3 O2 ? ? ? 1_555 A G2L 10 N2 ? ? A C2L 3 A G2L 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G2L 4 N1 ? ? ? 1_555 A C2L 9 N3 ? ? A G2L 4 A C2L 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G2L 4 N2 ? ? ? 1_555 A C2L 9 O2 ? ? A G2L 4 A C2L 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G2L 4 O6 ? ? ? 1_555 A C2L 9 N4 ? ? A G2L 4 A C2L 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A2L 5 N1 ? ? ? 1_555 A U2L 8 N3 ? ? A A2L 5 A U2L 8 1_555 ? ? ? ? ? ? 'A2L-U2L PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 C2L 1 A C2L 1 ? C ? 2 A G2L 2 A G2L 2 ? G ? 3 A C2L 3 A C2L 3 ? C ? 4 A G2L 4 A G2L 4 ? G ? 5 A A2L 5 A A2L 5 ? A ? 6 A A2L 6 A A2L 6 ? A ? 7 A U2L 7 A U2L 7 ? U ? 8 A U2L 8 A U2L 8 ? U ? 9 A C2L 9 A C2L 9 ? C ? 10 A G2L 10 A G2L 10 ? G ? 11 A C2L 11 A C2L 11 ? C ? 12 A G2L 12 A G2L 12 ? G ? # _pdbx_nmr_ensemble.entry_id 1XV6 _pdbx_nmr_ensemble.conformers_calculated_total_number 30 _pdbx_nmr_ensemble.conformers_submitted_total_number 30 _pdbx_nmr_ensemble.conformer_selection_criteria 'all calculated structures submitted' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1XV6 _pdbx_nmr_representative.conformer_id 18 _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '0.9mM hairpin, 100% D2O, 50mM NaCl' _pdbx_nmr_sample_details.solvent_system '100% D2O' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 303 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 7.4 _pdbx_nmr_exptl_sample_conditions.ionic_strength '50mM NaCl' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 DQF-COSY # _pdbx_nmr_details.entry_id 1XV6 _pdbx_nmr_details.text 'Structure was determined using standard 2D homo- and heteronuclear techniques.' # _pdbx_nmr_refine.entry_id 1XV6 _pdbx_nmr_refine.method 'simulated annealing, energy minimization' _pdbx_nmr_refine.details ;structures were refined by NMR restrained molecular dynamics in two stages using a generalized born (GB) implicit solvation model. The resulting structures were subjected to energy minimization. 2',5' phosphodiester linkages between residues, O3* of each ribose modified by methoxyethyl. ; _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal VNMR 6.1B collection Varian 1 Felix 2000 processing Accelerys 2 Amber 6 refinement 'Kollman et al.' 3 # 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 A2L "O2'" O N N 1 A2L "C2'" C N R 2 A2L "C1'" C N R 3 A2L "O4'" O N N 4 A2L "C4'" C N R 5 A2L "C5'" C N N 6 A2L "O5'" O N N 7 A2L P P N N 8 A2L OP1 O N N 9 A2L OP3 O N N 10 A2L OP2 O N N 11 A2L "C3'" C N S 12 A2L "O3'" O N N 13 A2L "CA'" C N N 14 A2L "CB'" C N N 15 A2L "OC'" O N N 16 A2L "CD'" C N N 17 A2L N9 N Y N 18 A2L C8 C Y N 19 A2L N7 N Y N 20 A2L C5 C Y N 21 A2L C4 C Y N 22 A2L N3 N Y N 23 A2L C2 C Y N 24 A2L N1 N Y N 25 A2L C6 C Y N 26 A2L N6 N N N 27 A2L "HO2'" H N N 28 A2L "H2'" H N N 29 A2L "H1'" H N N 30 A2L "H4'" H N N 31 A2L "H5'" H N N 32 A2L "H5''" H N N 33 A2L HOP3 H N N 34 A2L HOP2 H N N 35 A2L "H3'" H N N 36 A2L "HA'1" H N N 37 A2L "HA'2" H N N 38 A2L "HB'1" H N N 39 A2L "HB'2" H N N 40 A2L "HD'1" H N N 41 A2L "HD'2" H N N 42 A2L "HD'3" H N N 43 A2L H8 H N N 44 A2L H2 H N N 45 A2L H61 H N N 46 A2L H62 H N N 47 C2L OP3 O N N 48 C2L P P N N 49 C2L OP1 O N N 50 C2L OP2 O N N 51 C2L "O5'" O N N 52 C2L "C5'" C N N 53 C2L "C4'" C N R 54 C2L "O4'" O N N 55 C2L "C3'" C N S 56 C2L "O3'" O N N 57 C2L "C2'" C N R 58 C2L "O2'" O N N 59 C2L "C1'" C N R 60 C2L N1 N N N 61 C2L C2 C N N 62 C2L O2 O N N 63 C2L N3 N N N 64 C2L C4 C N N 65 C2L N4 N N N 66 C2L C5 C N N 67 C2L C6 C N N 68 C2L "CA'" C N N 69 C2L "CB'" C N N 70 C2L "OC'" O N N 71 C2L "CD'" C N N 72 C2L C7 C N N 73 C2L HOP3 H N N 74 C2L HOP2 H N N 75 C2L "H5'" H N N 76 C2L "H5''" H N N 77 C2L "H4'" H N N 78 C2L "H3'" H N N 79 C2L "H2'" H N N 80 C2L "HO2'" H N N 81 C2L "H1'" H N N 82 C2L H41 H N N 83 C2L H42 H N N 84 C2L H6 H N N 85 C2L "HA'1" H N N 86 C2L "HA'2" H N N 87 C2L "HB'1" H N N 88 C2L "HB'2" H N N 89 C2L "HD'1" H N N 90 C2L "HD'2" H N N 91 C2L "HD'3" H N N 92 C2L H71 H N N 93 C2L H72 H N N 94 C2L H73 H N N 95 G2L OP3 O N N 96 G2L P P N N 97 G2L OP1 O N N 98 G2L OP2 O N N 99 G2L "O5'" O N N 100 G2L "C5'" C N N 101 G2L "C4'" C N R 102 G2L "O4'" O N N 103 G2L "C3'" C N S 104 G2L "O3'" O N N 105 G2L "C2'" C N R 106 G2L "O2'" O N N 107 G2L "C1'" C N R 108 G2L N9 N Y N 109 G2L C8 C Y N 110 G2L N7 N Y N 111 G2L C5 C Y N 112 G2L C6 C N N 113 G2L O6 O N N 114 G2L N1 N N N 115 G2L C2 C N N 116 G2L N2 N N N 117 G2L N3 N N N 118 G2L C4 C Y N 119 G2L "CA'" C N N 120 G2L "CB'" C N N 121 G2L "OC'" O N N 122 G2L "CD'" C N N 123 G2L HOP3 H N N 124 G2L HOP2 H N N 125 G2L "H5'" H N N 126 G2L "H5''" H N N 127 G2L "H4'" H N N 128 G2L "H3'" H N N 129 G2L "H2'" H N N 130 G2L "HO2'" H N N 131 G2L "H1'" H N N 132 G2L H8 H N N 133 G2L H1 H N N 134 G2L H21 H N N 135 G2L H22 H N N 136 G2L "HA'1" H N N 137 G2L "HA'2" H N N 138 G2L "HB'1" H N N 139 G2L "HB'2" H N N 140 G2L "HD'1" H N N 141 G2L "HD'2" H N N 142 G2L "HD'3" H N N 143 U2L OP3 O N N 144 U2L P P N N 145 U2L OP1 O N N 146 U2L OP2 O N N 147 U2L "O5'" O N N 148 U2L "C5'" C N N 149 U2L "C4'" C N R 150 U2L "O4'" O N N 151 U2L "C3'" C N S 152 U2L "O3'" O N N 153 U2L "C2'" C N R 154 U2L "O2'" O N N 155 U2L "C1'" C N R 156 U2L N1 N N N 157 U2L C2 C N N 158 U2L O2 O N N 159 U2L N3 N N N 160 U2L C4 C N N 161 U2L O4 O N N 162 U2L C5 C N N 163 U2L C6 C N N 164 U2L "CA'" C N N 165 U2L "CB'" C N N 166 U2L "OC'" O N N 167 U2L "CD'" C N N 168 U2L C7 C N N 169 U2L HOP3 H N N 170 U2L HOP2 H N N 171 U2L "H5'" H N N 172 U2L "H5''" H N N 173 U2L "H4'" H N N 174 U2L "H3'" H N N 175 U2L "H2'" H N N 176 U2L "HO2'" H N N 177 U2L "H1'" H N N 178 U2L H3 H N N 179 U2L H6 H N N 180 U2L "HA'1" H N N 181 U2L "HA'2" H N N 182 U2L "HB'1" H N N 183 U2L "HB'2" H N N 184 U2L "HD'1" H N N 185 U2L "HD'2" H N N 186 U2L "HD'3" H N N 187 U2L H71 H N N 188 U2L H72 H N N 189 U2L H73 H N N 190 # 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 A2L "O2'" "C2'" sing N N 1 A2L "O2'" "HO2'" sing N N 2 A2L "C2'" "C1'" sing N N 3 A2L "C2'" "C3'" sing N N 4 A2L "C2'" "H2'" sing N N 5 A2L "C1'" "O4'" sing N N 6 A2L "C1'" N9 sing N N 7 A2L "C1'" "H1'" sing N N 8 A2L "O4'" "C4'" sing N N 9 A2L "C4'" "C5'" sing N N 10 A2L "C4'" "C3'" sing N N 11 A2L "C4'" "H4'" sing N N 12 A2L "C5'" "O5'" sing N N 13 A2L "C5'" "H5'" sing N N 14 A2L "C5'" "H5''" sing N N 15 A2L "O5'" P sing N N 16 A2L P OP1 doub N N 17 A2L P OP3 sing N N 18 A2L P OP2 sing N N 19 A2L OP3 HOP3 sing N N 20 A2L OP2 HOP2 sing N N 21 A2L "C3'" "O3'" sing N N 22 A2L "C3'" "H3'" sing N N 23 A2L "O3'" "CA'" sing N N 24 A2L "CA'" "CB'" sing N N 25 A2L "CA'" "HA'1" sing N N 26 A2L "CA'" "HA'2" sing N N 27 A2L "CB'" "OC'" sing N N 28 A2L "CB'" "HB'1" sing N N 29 A2L "CB'" "HB'2" sing N N 30 A2L "OC'" "CD'" sing N N 31 A2L "CD'" "HD'1" sing N N 32 A2L "CD'" "HD'2" sing N N 33 A2L "CD'" "HD'3" sing N N 34 A2L N9 C8 sing Y N 35 A2L N9 C4 sing Y N 36 A2L C8 N7 doub Y N 37 A2L C8 H8 sing N N 38 A2L N7 C5 sing Y N 39 A2L C5 C4 doub Y N 40 A2L C5 C6 sing Y N 41 A2L C4 N3 sing Y N 42 A2L N3 C2 doub Y N 43 A2L C2 N1 sing Y N 44 A2L C2 H2 sing N N 45 A2L N1 C6 doub Y N 46 A2L C6 N6 sing N N 47 A2L N6 H61 sing N N 48 A2L N6 H62 sing N N 49 C2L OP3 P sing N N 50 C2L OP3 HOP3 sing N N 51 C2L P OP1 doub N N 52 C2L P OP2 sing N N 53 C2L P "O5'" sing N N 54 C2L OP2 HOP2 sing N N 55 C2L "O5'" "C5'" sing N N 56 C2L "C5'" "C4'" sing N N 57 C2L "C5'" "H5'" sing N N 58 C2L "C5'" "H5''" sing N N 59 C2L "C4'" "O4'" sing N N 60 C2L "C4'" "C3'" sing N N 61 C2L "C4'" "H4'" sing N N 62 C2L "O4'" "C1'" sing N N 63 C2L "C3'" "O3'" sing N N 64 C2L "C3'" "C2'" sing N N 65 C2L "C3'" "H3'" sing N N 66 C2L "O3'" "CA'" sing N N 67 C2L "C2'" "O2'" sing N N 68 C2L "C2'" "C1'" sing N N 69 C2L "C2'" "H2'" sing N N 70 C2L "O2'" "HO2'" sing N N 71 C2L "C1'" N1 sing N N 72 C2L "C1'" "H1'" sing N N 73 C2L N1 C2 sing N N 74 C2L N1 C6 sing N N 75 C2L C2 O2 doub N N 76 C2L C2 N3 sing N N 77 C2L N3 C4 doub N N 78 C2L C4 N4 sing N N 79 C2L C4 C5 sing N N 80 C2L N4 H41 sing N N 81 C2L N4 H42 sing N N 82 C2L C5 C6 doub N N 83 C2L C5 C7 sing N N 84 C2L C6 H6 sing N N 85 C2L "CA'" "CB'" sing N N 86 C2L "CA'" "HA'1" sing N N 87 C2L "CA'" "HA'2" sing N N 88 C2L "CB'" "OC'" sing N N 89 C2L "CB'" "HB'1" sing N N 90 C2L "CB'" "HB'2" sing N N 91 C2L "OC'" "CD'" sing N N 92 C2L "CD'" "HD'1" sing N N 93 C2L "CD'" "HD'2" sing N N 94 C2L "CD'" "HD'3" sing N N 95 C2L C7 H71 sing N N 96 C2L C7 H72 sing N N 97 C2L C7 H73 sing N N 98 G2L OP3 P sing N N 99 G2L OP3 HOP3 sing N N 100 G2L P OP1 doub N N 101 G2L P OP2 sing N N 102 G2L P "O5'" sing N N 103 G2L OP2 HOP2 sing N N 104 G2L "O5'" "C5'" sing N N 105 G2L "C5'" "C4'" sing N N 106 G2L "C5'" "H5'" sing N N 107 G2L "C5'" "H5''" sing N N 108 G2L "C4'" "O4'" sing N N 109 G2L "C4'" "C3'" sing N N 110 G2L "C4'" "H4'" sing N N 111 G2L "O4'" "C1'" sing N N 112 G2L "C3'" "O3'" sing N N 113 G2L "C3'" "C2'" sing N N 114 G2L "C3'" "H3'" sing N N 115 G2L "O3'" "CA'" sing N N 116 G2L "C2'" "O2'" sing N N 117 G2L "C2'" "C1'" sing N N 118 G2L "C2'" "H2'" sing N N 119 G2L "O2'" "HO2'" sing N N 120 G2L "C1'" N9 sing N N 121 G2L "C1'" "H1'" sing N N 122 G2L N9 C8 sing Y N 123 G2L N9 C4 sing Y N 124 G2L C8 N7 doub Y N 125 G2L C8 H8 sing N N 126 G2L N7 C5 sing Y N 127 G2L C5 C6 sing N N 128 G2L C5 C4 doub Y N 129 G2L C6 O6 doub N N 130 G2L C6 N1 sing N N 131 G2L N1 C2 sing N N 132 G2L N1 H1 sing N N 133 G2L C2 N2 sing N N 134 G2L C2 N3 doub N N 135 G2L N2 H21 sing N N 136 G2L N2 H22 sing N N 137 G2L N3 C4 sing N N 138 G2L "CA'" "CB'" sing N N 139 G2L "CA'" "HA'1" sing N N 140 G2L "CA'" "HA'2" sing N N 141 G2L "CB'" "OC'" sing N N 142 G2L "CB'" "HB'1" sing N N 143 G2L "CB'" "HB'2" sing N N 144 G2L "OC'" "CD'" sing N N 145 G2L "CD'" "HD'1" sing N N 146 G2L "CD'" "HD'2" sing N N 147 G2L "CD'" "HD'3" sing N N 148 U2L OP3 P sing N N 149 U2L OP3 HOP3 sing N N 150 U2L P OP1 doub N N 151 U2L P OP2 sing N N 152 U2L P "O5'" sing N N 153 U2L OP2 HOP2 sing N N 154 U2L "O5'" "C5'" sing N N 155 U2L "C5'" "C4'" sing N N 156 U2L "C5'" "H5'" sing N N 157 U2L "C5'" "H5''" sing N N 158 U2L "C4'" "O4'" sing N N 159 U2L "C4'" "C3'" sing N N 160 U2L "C4'" "H4'" sing N N 161 U2L "O4'" "C1'" sing N N 162 U2L "C3'" "O3'" sing N N 163 U2L "C3'" "C2'" sing N N 164 U2L "C3'" "H3'" sing N N 165 U2L "O3'" "CA'" sing N N 166 U2L "C2'" "O2'" sing N N 167 U2L "C2'" "C1'" sing N N 168 U2L "C2'" "H2'" sing N N 169 U2L "O2'" "HO2'" sing N N 170 U2L "C1'" N1 sing N N 171 U2L "C1'" "H1'" sing N N 172 U2L N1 C2 sing N N 173 U2L N1 C6 sing N N 174 U2L C2 O2 doub N N 175 U2L C2 N3 sing N N 176 U2L N3 C4 sing N N 177 U2L N3 H3 sing N N 178 U2L C4 O4 doub N N 179 U2L C4 C5 sing N N 180 U2L C5 C6 doub N N 181 U2L C5 C7 sing N N 182 U2L C6 H6 sing N N 183 U2L "CA'" "CB'" sing N N 184 U2L "CA'" "HA'1" sing N N 185 U2L "CA'" "HA'2" sing N N 186 U2L "CB'" "OC'" sing N N 187 U2L "CB'" "HB'1" sing N N 188 U2L "CB'" "HB'2" sing N N 189 U2L "OC'" "CD'" sing N N 190 U2L "CD'" "HD'1" sing N N 191 U2L "CD'" "HD'2" sing N N 192 U2L "CD'" "HD'3" sing N N 193 U2L C7 H71 sing N N 194 U2L C7 H72 sing N N 195 U2L C7 H73 sing N N 196 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1XV6 'double helix' 1XV6 'hairpin loop' # 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 C2L 1 1_555 A G2L 12 1_555 -5.361 1.577 0.662 0.259 9.314 43.403 1 A_C2L1:G2L12_A A 1 ? A 12 ? ? ? 1 A G2L 2 1_555 A C2L 11 1_555 -0.899 -0.183 -0.137 -8.217 -17.005 0.132 2 A_G2L2:C2L11_A A 2 ? A 11 ? 19 1 1 A C2L 3 1_555 A G2L 10 1_555 0.742 -0.158 0.407 1.696 -9.297 -0.949 3 A_C2L3:G2L10_A A 3 ? A 10 ? 19 1 1 A G2L 4 1_555 A C2L 9 1_555 -0.305 -0.013 0.668 11.189 10.645 2.571 4 A_G2L4:C2L9_A A 4 ? A 9 ? 19 1 1 A A2L 5 1_555 A U2L 8 1_555 1.077 0.128 1.541 31.275 -11.219 13.286 5 A_A2L5:U2L8_A A 5 ? A 8 ? ? ? # 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 C2L 1 1_555 A G2L 12 1_555 A G2L 2 1_555 A C2L 11 1_555 -5.745 1.317 -0.878 106.190 -133.254 -55.816 -0.005 -2.358 3.659 68.623 54.685 -171.510 1 AA_C2L1G2L2:C2L11G2L12_AA A 1 ? A 12 ? A 2 ? A 11 ? 1 A G2L 2 1_555 A C2L 11 1_555 A C2L 3 1_555 A G2L 10 1_555 0.406 -1.411 2.973 -4.050 1.461 44.887 -1.958 -0.856 2.883 1.908 5.289 45.083 2 AA_G2L2C2L3:G2L10C2L11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A C2L 3 1_555 A G2L 10 1_555 A G2L 4 1_555 A C2L 9 1_555 0.860 -2.324 3.245 -2.111 -19.377 37.407 -0.905 -1.454 3.894 -28.008 3.051 42.019 3 AA_C2L3G2L4:C2L9G2L10_AA A 3 ? A 10 ? A 4 ? A 9 ? 1 A G2L 4 1_555 A C2L 9 1_555 A A2L 5 1_555 A U2L 8 1_555 -0.523 -0.745 2.901 -7.007 -7.511 44.851 -0.359 0.114 3.026 -9.694 9.043 45.953 4 AA_G2L4A2L5:U2L8C2L9_AA A 4 ? A 9 ? A 5 ? A 8 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.field_strength 600 # _atom_sites.entry_id 1XV6 _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_