data_7W9M # _model_server_result.job_id 5PkkfeL1yo3rKk7CJdY7Pg _model_server_result.datetime_utc '2024-11-22 00:41:54' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7w9m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2001}' # _entry.id 7W9M # _exptl.entry_id 7W9M _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 319.268 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name)' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7W9M _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W9M _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 E 1 NAG E 304 NAG 4 n D NAG 2 E 2 NAG E 305 NAG 4 n E NAG 1 D 1 NAG D 2007 NAG 4 n E NAG 2 D 2 NAG D 2008 NAG # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 318 A CYS 275 1_555 A SG CYS 367 A CYS 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 358 A CYS 315 1_555 A SG CYS 373 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 940 A CYS 897 1_555 A SG CYS 946 A CYS 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 978 A CYS 935 1_555 A SG CYS 987 A CYS 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 A SG CYS 1393 A CYS 1350 1_555 A SG CYS 1413 A CYS 1370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 A SG CYS 1758 A CYS 1715 1_555 A SG CYS 1773 A CYS 1730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 B SG CYS 21 B CYS 21 1_555 B SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 40 B CYS 40 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 C SG CYS 50 C CYS 50 1_555 C SG CYS 127 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf10 C SG CYS 72 C CYS 72 1_555 C SG CYS 75 C CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 326 A ASN 283 1_555 G C1 NAG . A NAG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 1395 A ASN 1352 1_555 E C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale3 A ND2 ASN 1409 A ASN 1366 1_555 H C1 NAG . A NAG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.583 ? covale ? covale4 A ND2 ASN 1418 A ASN 1375 1_555 N C1 NAG . A NAG 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.589 ? covale ? covale5 B ND2 ASN 93 B ASN 93 1_555 P C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale6 B ND2 ASN 110 B ASN 110 1_555 Q C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.564 ? covale ? covale7 B ND2 ASN 114 B ASN 114 1_555 R C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.597 ? covale ? covale8 B ND2 ASN 135 B ASN 135 1_555 D C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale9 D O4 NAG . E NAG 1 1_555 D C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale10 E O4 NAG . D NAG 1 1_555 E C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _chem_comp.formula 'C11 H17 N3 O8' _chem_comp.formula_weight 319.268 _chem_comp.id 9SR _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name)' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Tetrodotoxin # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N18 C13 9SR sing 1 n n N14 C13 9SR doub 2 n n N14 C15 9SR sing 3 n n O10 C09 9SR sing 4 n n C13 N12 9SR sing 5 n n O16 C15 9SR sing 6 n n C15 C17 9SR sing 7 n n N12 C11 9SR sing 8 n n C09 C11 9SR sing 9 n n C09 C07 9SR sing 10 n n O08 C07 9SR sing 11 n n C17 C11 9SR sing 12 n n C17 C05 9SR sing 13 n n C11 C19 9SR sing 14 n n O06 C07 9SR sing 15 n n O06 C05 9SR sing 16 n n C07 O01 9SR sing 17 n n C05 C03 9SR sing 18 n n C19 O20 9SR sing 19 n n C19 C02 9SR sing 20 n n O01 C02 9SR sing 21 n n C03 C02 9SR sing 22 n n C03 O04 9SR sing 23 n n C03 C21 9SR sing 24 n n O22 C21 9SR sing 25 n n C15 H1 9SR sing 26 n n C17 H2 9SR sing 27 n n C21 H3 9SR sing 28 n n C21 H4 9SR sing 29 n n C02 H5 9SR sing 30 n n C05 H6 9SR sing 31 n n C09 H7 9SR sing 32 n n C19 H8 9SR sing 33 n n N18 H10 9SR sing 34 n n N18 H11 9SR sing 35 n n O04 H12 9SR sing 36 n n O08 H13 9SR sing 37 n n O10 H14 9SR sing 38 n n O16 H15 9SR sing 39 n n O20 H16 9SR sing 40 n n O22 H17 9SR sing 41 n n N12 H18 9SR sing 42 n n # _atom_sites.entry_id 7W9M _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code F 5 9SR A 1 2001 1901 9SR TTX . G 6 NAG A 1 2002 2006 NAG NAG . H 6 NAG A 1 2003 2009 NAG NAG . I 7 P5S A 1 2004 2012 P5S P5S . J 8 Y01 A 1 2005 2015 Y01 Y01 . K 8 Y01 A 1 2006 2016 Y01 Y01 . L 8 Y01 A 1 2007 2017 Y01 Y01 . M 8 Y01 A 1 2008 2020 Y01 Y01 . N 6 NAG A 1 2009 2021 NAG NAG . O 8 Y01 A 1 2010 2022 Y01 Y01 . P 6 NAG B 1 301 301 NAG NAG . Q 6 NAG B 1 302 302 NAG NAG . R 6 NAG B 1 303 303 NAG NAG . S 9 LPE B 1 304 306 LPE LPE . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N12 9SR . . . F 5 135.276 134.862 142.388 1 44.54 ? N12 9SR 2001 A 1 HETATM 2 C C13 9SR . . . F 5 134.429 134.53 141.266 1 44.54 ? C13 9SR 2001 A 1 HETATM 3 C C15 9SR . . . F 5 134.854 132.044 141.773 1 44.54 ? C15 9SR 2001 A 1 HETATM 4 C C17 9SR . . . F 5 135.109 132.519 143.163 1 44.54 ? C17 9SR 2001 A 1 HETATM 5 C C21 9SR . . . F 5 136.88 130.765 146.105 1 44.54 ? C21 9SR 2001 A 1 HETATM 6 C C02 9SR . . . F 5 136.81 133.164 145.363 1 44.54 ? C02 9SR 2001 A 1 HETATM 7 C C03 9SR . . . F 5 136.073 131.916 145.285 1 44.54 ? C03 9SR 2001 A 1 HETATM 8 C C05 9SR . . . F 5 135.948 131.484 143.908 1 44.54 ? C05 9SR 2001 A 1 HETATM 9 C C07 9SR . . . F 5 137.992 132.644 143.337 1 44.54 ? C07 9SR 2001 A 1 HETATM 10 C C09 9SR . . . F 5 137.335 133.649 142.552 1 44.54 ? C09 9SR 2001 A 1 HETATM 11 C C11 9SR . . . F 5 135.885 133.857 143.142 1 44.54 ? C11 9SR 2001 A 1 HETATM 12 C C19 9SR . . . F 5 136.046 134.282 144.626 1 44.54 ? C19 9SR 2001 A 1 HETATM 13 N N14 9SR . . . F 5 134.189 133.087 140.932 1 44.54 ? N14 9SR 2001 A 1 HETATM 14 N N18 9SR . . . F 5 133.806 135.573 140.481 1 44.54 ? N18 9SR 2001 A 1 HETATM 15 O O01 9SR . . . F 5 138.054 133.096 144.729 1 44.54 ? O01 9SR 2001 A 1 HETATM 16 O O04 9SR . . . F 5 134.819 132.05 145.859 1 44.54 ? O04 9SR 2001 A 1 HETATM 17 O O06 9SR . . . F 5 137.183 131.46 143.225 1 44.54 ? O06 9SR 2001 A 1 HETATM 18 O O08 9SR . . . F 5 139.256 132.44 142.805 1 44.54 ? O08 9SR 2001 A 1 HETATM 19 O O10 9SR . . . F 5 137.271 133.142 141.27 1 44.54 ? O10 9SR 2001 A 1 HETATM 20 O O16 9SR . . . F 5 134.011 130.949 141.887 1 44.54 ? O16 9SR 2001 A 1 HETATM 21 O O20 9SR . . . F 5 136.795 135.405 144.644 1 44.54 ? O20 9SR 2001 A 1 HETATM 22 O O22 9SR . . . F 5 138.153 130.658 145.55 1 44.54 ? O22 9SR 2001 A 1 # _model_server_stats.io_time_ms 143 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 67 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 22 #