data_1Y29 # _entry.id 1Y29 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1Y29 pdb_00001y29 10.2210/pdb1y29/pdb RCSB RCSB031024 ? ? WWPDB D_1000031024 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Y29 _pdbx_database_status.recvd_initial_deposition_date 2004-11-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _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 'Liu, Z.' 1 'Liang, S.' 2 # _citation.id primary _citation.title ;Function and solution structure of Huwentoxin-X, a specific blocker of N-type calcium channels, from the Chinese bird spider Ornithoctonus huwena ; _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 281 _citation.page_first 8628 _citation.page_last 8635 _citation.year 2006 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16439354 _citation.pdbx_database_id_DOI 10.1074/jbc.M513542200 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Liu, Z.' 1 ? primary 'Dai, J.' 2 ? primary 'Dai, L.' 3 ? primary 'Deng, M.' 4 ? primary 'Hu, Z.' 5 ? primary 'Hu, W.' 6 ? primary 'Liang, S.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description huwentoxin-x _entity.formula_weight 2942.567 _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 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code KCLPPGKPCYGATQKIPCCGVCSHNKCT _entity_poly.pdbx_seq_one_letter_code_can KCLPPGKPCYGATQKIPCCGVCSHNKCT _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 CYS n 1 3 LEU n 1 4 PRO n 1 5 PRO n 1 6 GLY n 1 7 LYS n 1 8 PRO n 1 9 CYS n 1 10 TYR n 1 11 GLY n 1 12 ALA n 1 13 THR n 1 14 GLN n 1 15 LYS n 1 16 ILE n 1 17 PRO n 1 18 CYS n 1 19 CYS n 1 20 GLY n 1 21 VAL n 1 22 CYS n 1 23 SER n 1 24 HIS n 1 25 ASN n 1 26 LYS n 1 27 CYS n 1 28 THR 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 'This peptide was isolated from the venom of spider Ornithoctonus huwena, synthesized by using solid phase chemical method.' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TXH10_ORNHU _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code KCLPPGKPCYGATQKIPCCGVCSHNKCT _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession P68424 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1Y29 _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 28 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P68424 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 28 _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 28 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 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 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 DQF-COSY 2 1 1 '2D TOCSY' 3 1 1 '2D NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 4.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength 20 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '5MM HUWENTOXIN-X; PHOSPHATE BUFFER' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DMX _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1Y29 _pdbx_nmr_refine.method 'distance geometry, simulated annealing' _pdbx_nmr_refine.details ;The structures are based on 261 noe-derived distance constraints, 10 dihedral angel restraints and 9 fake distance restraints from disulfide bonds. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1Y29 _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _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 1Y29 _pdbx_nmr_representative.conformer_id 6 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal NMRView 5.0 'data analysis' 'Bruce A. Johnson' 1 X-PLOR NIH-2.9.6 refinement 'C.D. Schwieters' 2 # _exptl.entry_id 1Y29 _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 # _struct.entry_id 1Y29 _struct.title 'Three dimensional solution structure of huwentoxin-x by 2D 1H-NMR' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Y29 _struct_keywords.pdbx_keywords TOXIN _struct_keywords.text 'A double-stranded beta-sheet, ICK, Knottin, 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 # 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 disulf1 disulf ? ? A CYS 2 SG ? ? ? 1_555 A CYS 19 SG ? ? A CYS 2 A CYS 19 1_555 ? ? ? ? ? ? ? 2.022 ? ? disulf2 disulf ? ? A CYS 9 SG ? ? ? 1_555 A CYS 22 SG ? ? A CYS 9 A CYS 22 1_555 ? ? ? ? ? ? ? 2.022 ? ? disulf3 disulf ? ? A CYS 18 SG ? ? ? 1_555 A CYS 27 SG ? ? A CYS 18 A CYS 27 1_555 ? ? ? ? ? ? ? 2.018 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1Y29 _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 # _atom_sites.entry_id 1Y29 _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 S # 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 CYS 2 2 2 CYS CYS A . n A 1 3 LEU 3 3 3 LEU LEU A . n A 1 4 PRO 4 4 4 PRO PRO A . n A 1 5 PRO 5 5 5 PRO PRO A . n A 1 6 GLY 6 6 6 GLY GLY A . n A 1 7 LYS 7 7 7 LYS LYS A . n A 1 8 PRO 8 8 8 PRO PRO A . n A 1 9 CYS 9 9 9 CYS CYS A . n A 1 10 TYR 10 10 10 TYR TYR A . n A 1 11 GLY 11 11 11 GLY GLY A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 THR 13 13 13 THR THR A . n A 1 14 GLN 14 14 14 GLN GLN A . n A 1 15 LYS 15 15 15 LYS LYS A . n A 1 16 ILE 16 16 16 ILE ILE A . n A 1 17 PRO 17 17 17 PRO PRO A . n A 1 18 CYS 18 18 18 CYS CYS A . n A 1 19 CYS 19 19 19 CYS CYS A . n A 1 20 GLY 20 20 20 GLY GLY A . n A 1 21 VAL 21 21 21 VAL VAL A . n A 1 22 CYS 22 22 22 CYS CYS A . n A 1 23 SER 23 23 23 SER SER A . n A 1 24 HIS 24 24 24 HIS HIS A . n A 1 25 ASN 25 25 25 ASN ASN A . n A 1 26 LYS 26 26 26 LYS LYS A . n A 1 27 CYS 27 27 27 CYS CYS A . n A 1 28 THR 28 28 28 THR THR 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 2004-12-07 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Experimental preparation' # 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_exptl_sample_conditions 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # 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_exptl_sample_conditions.pressure_units' # 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 THR A 13 ? ? -106.44 71.01 2 2 THR A 13 ? ? -177.49 59.57 3 4 THR A 13 ? ? -170.88 63.01 4 5 ALA A 12 ? ? -141.33 49.48 5 5 THR A 13 ? ? 56.09 91.95 6 6 THR A 13 ? ? -154.86 70.25 7 8 THR A 13 ? ? 60.35 107.05 8 10 THR A 13 ? ? -173.31 66.17 9 11 THR A 13 ? ? -173.81 69.84 10 11 SER A 23 ? ? -88.89 -132.71 11 11 HIS A 24 ? ? -67.11 74.42 12 12 THR A 13 ? ? -174.82 59.50 13 12 SER A 23 ? ? -95.41 -138.69 14 12 HIS A 24 ? ? -69.35 76.88 15 14 GLN A 14 ? ? -172.00 137.17 16 18 THR A 13 ? ? -150.27 64.67 17 18 SER A 23 ? ? -100.12 -139.57 18 19 GLN A 14 ? ? -163.48 117.38 #