data_2N85 # _entry.id 2N85 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_code _database_2.database_id _database_2.pdbx_database_accession _database_2.pdbx_DOI RCSB104542 RCSB ? ? 2N85 PDB pdb_00002n85 10.2210/pdb2n85/pdb 25835 BMRB ? ? D_1000104542 WWPDB ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 25835 BMRB unspecified . 2N86 PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2N85 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2015-10-05 _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 REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nadezhdin, K.' 1 'Romanovskaya, D.' 2 'Sachkova, M.' 3 'Vassilevski, A.' 4 'Grishin, E.' 5 'Kovalchuk, S.' 6 'Arseniev, A.' 7 # _citation.id primary _citation.title 'Modular toxin from the lynx spider Oxyopes takobius: Structure of spiderine domains in solution and membrane-mimicking environment.' _citation.journal_abbrev 'Protein Sci.' _citation.journal_volume 26 _citation.page_first 611 _citation.page_last 616 _citation.year 2017 _citation.journal_id_ASTM PRCIEI _citation.country US _citation.journal_id_ISSN 1469-896X _citation.journal_id_CSD 0795 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 27997708 _citation.pdbx_database_id_DOI 10.1002/pro.3101 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nadezhdin, K.D.' 1 ? primary 'Romanovskaia, D.D.' 2 ? primary 'Sachkova, M.Y.' 3 ? primary 'Oparin, P.B.' 4 ? primary 'Kovalchuk, S.I.' 5 ? primary 'Grishin, E.V.' 6 ? primary 'Arseniev, A.S.' 7 ? primary 'Vassilevski, A.A.' 8 0000-0002-1359-0076 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description Spiderine-1a _entity.formula_weight 4832.002 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'UNP residues 59-99' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name OtTx1a # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code KFKWGKLFSTAKKLYKKGKKLSKNKNFKKALKFGKQLAKNL _entity_poly.pdbx_seq_one_letter_code_can KFKWGKLFSTAKKLYKKGKKLSKNKNFKKALKFGKQLAKNL _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 LYS n 1 2 PHE n 1 3 LYS n 1 4 TRP n 1 5 GLY n 1 6 LYS n 1 7 LEU n 1 8 PHE n 1 9 SER n 1 10 THR n 1 11 ALA n 1 12 LYS n 1 13 LYS n 1 14 LEU n 1 15 TYR n 1 16 LYS n 1 17 LYS n 1 18 GLY n 1 19 LYS n 1 20 LYS n 1 21 LEU n 1 22 SER n 1 23 LYS n 1 24 ASN n 1 25 LYS n 1 26 ASN n 1 27 PHE n 1 28 LYS n 1 29 LYS n 1 30 ALA n 1 31 LEU n 1 32 LYS n 1 33 PHE n 1 34 GLY n 1 35 LYS n 1 36 GLN n 1 37 LEU n 1 38 ALA n 1 39 LYS n 1 40 ASN n 1 41 LEU 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 'Oxyopes takobius' _pdbx_entity_src_syn.organism_common_name 'Lynx spider' _pdbx_entity_src_syn.ncbi_taxonomy_id 666126 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SPN1A_OXYTA _struct_ref.pdbx_db_accession P86716 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code KFKWGKLFSTAKKLYKKGKKLSKNKNFKKALKFGKQLAKNL _struct_ref.pdbx_align_begin 59 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2N85 _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 41 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P86716 _struct_ref_seq.db_align_beg 59 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 99 _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 41 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-13C HSQC' 1 2 1 '2D 1H-1H TOCSY' 1 3 1 '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH 3.3 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 313 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '0.6 mM protein, 60 mM DPC, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2N85 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _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 'target function' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2N85 _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 2N85 _pdbx_nmr_representative.selection_criteria 'fewest violations' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Koradi, Billeter and Wuthrich' 'structure solution' MOLMOL ? 1 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA ? 2 'Keller and Wuthrich' 'chemical shift assignment' CARA ? 3 'Cornilescu, Delaglio and Bax' 'angle prediction' TALOS ? 4 'Bruker Biospin' collection TopSpin ? 5 'Bruker Biospin' processing TopSpin ? 6 'Bruker Biospin' 'data analysis' TopSpin ? 7 'Guntert, Mumenthaler and Wuthrich' refinement CYANA ? 8 # _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 2N85 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2N85 _struct.title 'NMR structure of OtTx1a - AMP in DPC micelles' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2N85 _struct_keywords.pdbx_keywords TOXIN _struct_keywords.text 'Spider venom, N-terminal end, DPC micelles, TOXIN' # _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_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 LYS A 3 ? ASN A 24 ? LYS A 3 ASN A 24 1 ? 22 HELX_P HELX_P2 2 LYS A 25 ? ASN A 40 ? LYS A 25 ASN A 40 1 ? 16 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2N85 _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 # 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 LYS 1 1 1 LYS LYS A . n A 1 2 PHE 2 2 2 PHE PHE A . n A 1 3 LYS 3 3 3 LYS LYS A . n A 1 4 TRP 4 4 4 TRP TRP A . n A 1 5 GLY 5 5 5 GLY GLY A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 LEU 7 7 7 LEU LEU A . n A 1 8 PHE 8 8 8 PHE PHE A . n A 1 9 SER 9 9 9 SER SER A . n A 1 10 THR 10 10 10 THR THR A . n A 1 11 ALA 11 11 11 ALA ALA A . n A 1 12 LYS 12 12 12 LYS LYS A . n A 1 13 LYS 13 13 13 LYS LYS A . n A 1 14 LEU 14 14 14 LEU LEU A . n A 1 15 TYR 15 15 15 TYR TYR A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 LYS 17 17 17 LYS LYS A . n A 1 18 GLY 18 18 18 GLY GLY A . n A 1 19 LYS 19 19 19 LYS LYS A . n A 1 20 LYS 20 20 20 LYS LYS A . n A 1 21 LEU 21 21 21 LEU LEU A . n A 1 22 SER 22 22 22 SER SER A . n A 1 23 LYS 23 23 23 LYS LYS A . n A 1 24 ASN 24 24 24 ASN ASN A . n A 1 25 LYS 25 25 25 LYS LYS A . n A 1 26 ASN 26 26 26 ASN ASN A . n A 1 27 PHE 27 27 27 PHE PHE A . n A 1 28 LYS 28 28 28 LYS LYS A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 ALA 30 30 30 ALA ALA A . n A 1 31 LEU 31 31 31 LEU LEU A . n A 1 32 LYS 32 32 32 LYS LYS A . n A 1 33 PHE 33 33 33 PHE PHE A . n A 1 34 GLY 34 34 34 GLY GLY A . n A 1 35 LYS 35 35 35 LYS LYS A . n A 1 36 GLN 36 36 36 GLN GLN A . n A 1 37 LEU 37 37 37 LEU LEU A . n A 1 38 ALA 38 38 38 ALA ALA A . n A 1 39 LYS 39 39 39 LYS LYS A . n A 1 40 ASN 40 40 40 ASN ASN A . n A 1 41 LEU 41 41 41 LEU LEU A . n # _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 # 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 2016-10-05 2 'Structure model' 1 1 2019-04-17 3 'Structure model' 1 2 2023-06-14 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 3 'Structure model' Other # 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 2 'Structure model' pdbx_nmr_software 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_database_status 6 3 'Structure model' pdbx_nmr_spectrometer # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.journal_volume' 7 2 'Structure model' '_citation.page_first' 8 2 'Structure model' '_citation.page_last' 9 2 'Structure model' '_citation.pdbx_database_id_DOI' 10 2 'Structure model' '_citation.pdbx_database_id_PubMed' 11 2 'Structure model' '_citation.title' 12 2 'Structure model' '_citation.year' 13 2 'Structure model' '_pdbx_nmr_software.name' 14 3 'Structure model' '_database_2.pdbx_DOI' 15 3 'Structure model' '_database_2.pdbx_database_accession' 16 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 17 3 'Structure model' '_pdbx_nmr_spectrometer.model' # 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 protein-1 0.6 ? mM ? 1 DPC-2 60 ? mM ? 1 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASN A 24 ? ? -69.26 -169.08 2 2 ASN A 24 ? ? -53.27 105.53 3 3 ASN A 24 ? ? -63.70 -173.65 4 5 LYS A 23 ? ? -142.84 31.79 5 6 PHE A 2 ? ? 62.92 104.47 6 6 LYS A 23 ? ? -99.58 33.36 7 6 ASN A 40 ? ? -143.01 39.78 8 7 ASN A 24 ? ? -59.86 106.13 9 9 ASN A 24 ? ? -60.08 99.81 10 10 ASN A 24 ? ? -61.82 -168.88 11 14 PHE A 2 ? ? 61.20 99.77 12 14 LYS A 23 ? ? -67.48 -75.10 13 16 ASN A 24 ? ? -67.16 -169.16 14 17 LYS A 23 ? ? -68.57 -75.12 15 18 LYS A 23 ? ? -52.31 -76.70 16 18 ASN A 24 ? ? -144.28 19.93 #