data_2L13 # _entry.id 2L13 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2L13 pdb_00002l13 10.2210/pdb2l13/pdb RCSB RCSB101823 ? ? WWPDB D_1000101823 ? ? # 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 2011-07-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-05-01 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_nmr_software 5 3 'Structure model' struct_conn # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_nmr_software.name' 4 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2L13 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-07-22 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Siegmund, K.H.' 1 'Hariharan, M.' 2 'Lewis, F.D.' 3 # _citation.id primary _citation.title 'Conformation of a dodecane DNA hairpin linker. Multiple gauche bonds cover the bases.' _citation.journal_abbrev J.Phys.Chem.B _citation.journal_volume 115 _citation.page_first 3740 _citation.page_last 3746 _citation.year 2011 _citation.journal_id_ASTM JPCBFK _citation.country US _citation.journal_id_ISSN 1089-5647 _citation.journal_id_CSD 1278 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21410196 _citation.pdbx_database_id_DOI 10.1021/jp201188f # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Siegmund, K.' 1 ? primary 'Hariharan, M.' 2 ? primary 'Lewis, F.D.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3') ; _entity.formula_weight 3923.739 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 '(DT)(DA)(DT)(DT)(DA)(DT)(K12)(DA)(DT)(DA)(DA)(DT)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TATTATXATAATA _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 DT n 1 2 DA n 1 3 DT n 1 4 DT n 1 5 DA n 1 6 DT n 1 7 K12 n 1 8 DA n 1 9 DT n 1 10 DA n 1 11 DA n 1 12 DT n 1 13 DA n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 K12 non-polymer . '12-hydroxydodecyl dihydrogen phosphate' ? 'C12 H27 O5 P' 282.314 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DT 1 1 1 DT DT A . n A 1 2 DA 2 2 2 DA DA A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DT 4 4 4 DT DT A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 K12 7 7 7 K12 K12 A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DA 10 10 10 DA DA A . n A 1 11 DA 11 11 11 DA DA A . n A 1 12 DT 12 12 12 DT DT A . n A 1 13 DA 13 13 13 DA DA A . n # _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 ;The C12-alkyl linker enables the short sequence to form a stable mini-hairpin. Ring-currents of the neighboring base-pair made assignment for all methylene protons possible. The position of the last terminal base-pair is not well defined due to end-fraying and the resulting lack of a sufficient number of constraints. ; _exptl.entry_id 2L13 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2L13 _struct.title 'mini-haipin of AT basepairs having a C12-alkyl linker forming the loop region' _struct.pdbx_model_details 'minimized average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2L13 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'mini-hairpin, alkyl chain, C12, dodecyl, synthetic hybrid, DNA' # _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.db_code 2L13 _struct_ref.db_name PDB _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession 2L13 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code TATTATXATAATA _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2L13 _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 13 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2L13 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 13 _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 13 # _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 _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 DT 6 "O3'" ? ? ? 1_555 A K12 7 P ? ? A DT 6 A K12 7 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale both ? A K12 7 "O3'" ? ? ? 1_555 A DA 8 P ? ? A K12 7 A DA 8 1_555 ? ? ? ? ? ? ? 1.592 ? ? hydrog1 hydrog ? ? A DT 1 N3 ? ? ? 1_555 A DA 13 N1 ? ? A DT 1 A DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 A DA 13 N6 ? ? A DT 1 A DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DA 2 N1 ? ? ? 1_555 A DT 12 N3 ? ? A DA 2 A DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N6 ? ? ? 1_555 A DT 12 O4 ? ? A DA 2 A DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 3 N3 ? ? ? 1_555 A DA 11 N1 ? ? A DT 3 A DA 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 3 O4 ? ? ? 1_555 A DA 11 N6 ? ? A DT 3 A DA 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 4 N3 ? ? ? 1_555 A DA 10 N1 ? ? A DT 4 A DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 4 O4 ? ? ? 1_555 A DA 10 N6 ? ? A DT 4 A DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A DT 9 N3 ? ? A DA 5 A DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A DT 9 O4 ? ? A DA 5 A DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 6 N3 ? ? ? 1_555 A DA 8 N1 ? ? A DT 6 A DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 6 O4 ? ? ? 1_555 A DA 8 N6 ? ? A DT 6 A DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_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 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 2 O4 A DT 6 ? ? H62 A DA 8 ? ? 1.59 2 3 H3 A DT 6 ? ? N1 A DA 8 ? ? 1.58 3 5 H3 A DT 6 ? ? N1 A DA 8 ? ? 1.58 # _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 80 _pdbx_nmr_ensemble.conformers_submitted_total_number 11 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2L13 _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 2L13 _pdbx_nmr_representative.selection_criteria 'minimized average' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;4.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-1, 100% D2O ; 1 '100% D2O' ;4.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-2, 90% H2O/10% D2O ; 2 '90% H2O/10% D2O' # 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 ;DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-1 ; 4.2 ? mM ? 1 ;DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-2 ; 4.2 ? mM ? 2 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.1 _pdbx_nmr_exptl_sample_conditions.pH 7.2 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 293 _pdbx_nmr_exptl_sample_conditions.temperature_units K # 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 TOCSY' 1 3 1 '2D 1H-1H NOESY' 1 4 2 '2D DQF-COSY' 1 5 2 '2D 1H-1H TOCSY' 1 6 2 '2D 1H-1H NOESY' # _pdbx_nmr_refine.entry_id 2L13 _pdbx_nmr_refine.method 'simulated annealing, matrix relaxation' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.2 1 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNS 1.2 2 Goddard 'chemical shift assignment' Sparky 3.113 3 Goddard 'data analysis' Sparky 3.113 4 Goddard 'peak picking' Sparky 3.113 5 Goddard 'peak integration' Sparky 3.113 6 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe ? 7 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DT OP3 O N N 37 DT P P N N 38 DT OP1 O N N 39 DT OP2 O N N 40 DT "O5'" O N N 41 DT "C5'" C N N 42 DT "C4'" C N R 43 DT "O4'" O N N 44 DT "C3'" C N S 45 DT "O3'" O N N 46 DT "C2'" C N N 47 DT "C1'" C N R 48 DT N1 N N N 49 DT C2 C N N 50 DT O2 O N N 51 DT N3 N N N 52 DT C4 C N N 53 DT O4 O N N 54 DT C5 C N N 55 DT C7 C N N 56 DT C6 C N N 57 DT HOP3 H N N 58 DT HOP2 H N N 59 DT "H5'" H N N 60 DT "H5''" H N N 61 DT "H4'" H N N 62 DT "H3'" H N N 63 DT "HO3'" H N N 64 DT "H2'" H N N 65 DT "H2''" H N N 66 DT "H1'" H N N 67 DT H3 H N N 68 DT H71 H N N 69 DT H72 H N N 70 DT H73 H N N 71 DT H6 H N N 72 K12 P P N N 73 K12 C1 C N N 74 K12 C2 C N N 75 K12 C3 C N N 76 K12 C4 C N N 77 K12 C5 C N N 78 K12 C6 C N N 79 K12 C7 C N N 80 K12 C8 C N N 81 K12 C9 C N N 82 K12 C10 C N N 83 K12 C11 C N N 84 K12 C12 C N N 85 K12 "O3'" O N N 86 K12 "O5'" O N N 87 K12 OP1 O N N 88 K12 OP2 O N N 89 K12 H10 H N N 90 K12 H10A H N N 91 K12 H1 H N N 92 K12 H11 H N N 93 K12 H1A H N N 94 K12 H11A H N N 95 K12 H2 H N N 96 K12 H12 H N N 97 K12 H2A H N N 98 K12 H12A H N N 99 K12 H3 H N N 100 K12 H3A H N N 101 K12 H4 H N N 102 K12 H4A H N N 103 K12 H5 H N N 104 K12 H5A H N N 105 K12 H6 H N N 106 K12 H6A H N N 107 K12 H7 H N N 108 K12 H7A H N N 109 K12 H8 H N N 110 K12 H8A H N N 111 K12 H9 H N N 112 K12 H9A H N N 113 K12 OP3 O N N 114 K12 "HO3'" H N N 115 K12 HOP2 H N N 116 K12 HOP3 H N N 117 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DT OP3 P sing N N 39 DT OP3 HOP3 sing N N 40 DT P OP1 doub N N 41 DT P OP2 sing N N 42 DT P "O5'" sing N N 43 DT OP2 HOP2 sing N N 44 DT "O5'" "C5'" sing N N 45 DT "C5'" "C4'" sing N N 46 DT "C5'" "H5'" sing N N 47 DT "C5'" "H5''" sing N N 48 DT "C4'" "O4'" sing N N 49 DT "C4'" "C3'" sing N N 50 DT "C4'" "H4'" sing N N 51 DT "O4'" "C1'" sing N N 52 DT "C3'" "O3'" sing N N 53 DT "C3'" "C2'" sing N N 54 DT "C3'" "H3'" sing N N 55 DT "O3'" "HO3'" sing N N 56 DT "C2'" "C1'" sing N N 57 DT "C2'" "H2'" sing N N 58 DT "C2'" "H2''" sing N N 59 DT "C1'" N1 sing N N 60 DT "C1'" "H1'" sing N N 61 DT N1 C2 sing N N 62 DT N1 C6 sing N N 63 DT C2 O2 doub N N 64 DT C2 N3 sing N N 65 DT N3 C4 sing N N 66 DT N3 H3 sing N N 67 DT C4 O4 doub N N 68 DT C4 C5 sing N N 69 DT C5 C7 sing N N 70 DT C5 C6 doub N N 71 DT C7 H71 sing N N 72 DT C7 H72 sing N N 73 DT C7 H73 sing N N 74 DT C6 H6 sing N N 75 K12 P "O5'" sing N N 76 K12 P OP1 doub N N 77 K12 P OP2 sing N N 78 K12 C1 C2 sing N N 79 K12 C1 "O5'" sing N N 80 K12 C1 H1 sing N N 81 K12 C1 H1A sing N N 82 K12 C2 C3 sing N N 83 K12 C2 H2 sing N N 84 K12 C2 H2A sing N N 85 K12 C3 C4 sing N N 86 K12 C3 H3 sing N N 87 K12 C3 H3A sing N N 88 K12 C4 C5 sing N N 89 K12 C4 H4 sing N N 90 K12 C4 H4A sing N N 91 K12 C5 C6 sing N N 92 K12 C5 H5 sing N N 93 K12 C5 H5A sing N N 94 K12 C6 C7 sing N N 95 K12 C6 H6 sing N N 96 K12 C6 H6A sing N N 97 K12 C7 C8 sing N N 98 K12 C7 H7 sing N N 99 K12 C7 H7A sing N N 100 K12 C8 C9 sing N N 101 K12 C8 H8 sing N N 102 K12 C8 H8A sing N N 103 K12 C9 C10 sing N N 104 K12 C9 H9 sing N N 105 K12 C9 H9A sing N N 106 K12 C10 C11 sing N N 107 K12 C10 H10 sing N N 108 K12 C10 H10A sing N N 109 K12 C11 C12 sing N N 110 K12 C11 H11 sing N N 111 K12 C11 H11A sing N N 112 K12 C12 "O3'" sing N N 113 K12 C12 H12 sing N N 114 K12 C12 H12A sing N N 115 K12 P OP3 sing N N 116 K12 "O3'" "HO3'" sing N N 117 K12 OP2 HOP2 sing N N 118 K12 OP3 HOP3 sing N N 119 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2L13 'double helix' 2L13 'b-form double helix' 2L13 '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 DT 1 1_555 A DA 13 1_555 -0.361 -0.053 0.089 -1.489 -3.474 -4.145 1 A_DT1:DA13_A A 1 ? A 13 ? 20 1 1 A DA 2 1_555 A DT 12 1_555 0.092 -0.108 -0.126 -3.482 1.603 4.287 2 A_DA2:DT12_A A 2 ? A 12 ? 20 1 1 A DT 3 1_555 A DA 11 1_555 0.284 -0.203 -0.112 4.676 -3.564 6.151 3 A_DT3:DA11_A A 3 ? A 11 ? 20 1 1 A DT 4 1_555 A DA 10 1_555 0.539 -0.226 0.214 -5.636 -13.876 -5.331 4 A_DT4:DA10_A A 4 ? A 10 ? 20 1 1 A DA 5 1_555 A DT 9 1_555 -0.181 -0.053 -0.229 5.220 -3.518 1.268 5 A_DA5:DT9_A A 5 ? A 9 ? 20 1 1 A DT 6 1_555 A DA 8 1_555 0.106 -0.239 -0.320 22.052 -18.860 4.187 6 A_DT6:DA8_A A 6 ? A 8 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DT 1 1_555 A DA 13 1_555 A DA 2 1_555 A DT 12 1_555 -0.526 0.509 4.891 -1.583 -34.194 38.974 4.059 0.445 3.451 -42.664 1.976 51.428 1 AA_DT1DA2:DT12DA13_AA A 1 ? A 13 ? A 2 ? A 12 ? 1 A DA 2 1_555 A DT 12 1_555 A DT 3 1_555 A DA 11 1_555 0.208 -0.836 3.205 -3.403 -3.701 33.408 -0.845 -0.904 3.240 -6.393 5.878 33.774 2 AA_DA2DT3:DA11DT12_AA A 2 ? A 12 ? A 3 ? A 11 ? 1 A DT 3 1_555 A DA 11 1_555 A DT 4 1_555 A DA 10 1_555 -1.019 -0.864 3.734 2.491 0.058 36.373 -1.390 2.019 3.657 0.093 -3.985 36.455 3 AA_DT3DT4:DA10DA11_AA A 3 ? A 11 ? A 4 ? A 10 ? 1 A DT 4 1_555 A DA 10 1_555 A DA 5 1_555 A DT 9 1_555 1.047 -0.703 3.029 7.413 11.311 25.984 -3.673 -0.581 2.692 23.259 -15.242 29.239 4 AA_DT4DA5:DT9DA10_AA A 4 ? A 10 ? A 5 ? A 9 ? 1 A DA 5 1_555 A DT 9 1_555 A DT 6 1_555 A DA 8 1_555 -0.168 0.086 2.593 2.578 -2.991 35.161 0.489 0.577 2.559 -4.932 -4.250 35.375 5 AA_DA5DT6:DA8DT9_AA A 5 ? A 9 ? A 6 ? A 8 ? # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Varian INOVA' # _atom_sites.entry_id 2L13 _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_