data_6A95 # _model_server_result.job_id c9LCEKAzERSuYJEuOJ7zvg _model_server_result.datetime_utc '2024-11-21 14:00:23' _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 6a95 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1608}' # _entry.id 6A95 # _exptl.entry_id 6A95 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 319.268 _entity.id 5 _entity.src_method nat _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 6A95 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6A95 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 3 n C NAG 1 C 1 NAG A 1601 NAG 3 n C NAG 2 C 2 NAG A 1602 NAG 3 n D NAG 1 D 1 NAG A 1603 NAG 3 n D NAG 2 D 2 NAG A 1604 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 331 A CYS 288 1_555 A SG CYS 380 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 371 A CYS 328 1_555 A SG CYS 386 A CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 752 A CYS 709 1_555 A SG CYS 760 A CYS 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 1054 A CYS 1011 1_555 A SG CYS 1073 A CYS 1030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 1411 A CYS 1368 1_555 A SG CYS 1424 A CYS 1381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 B SG CYS 13 B CYS 13 1_555 B SG CYS 26 B CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 20 B CYS 20 1_555 B SG CYS 40 B CYS 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 B SG CYS 42 B CYS 42 1_555 B SG CYS 52 B CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 351 A ASN 308 1_555 G C1 NAG . A NAG 1607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale2 A ND2 ASN 355 A ASN 312 1_555 F C1 NAG . A NAG 1606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale3 A ND2 ASN 373 A ASN 330 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale4 A ND2 ASN 1058 A ASN 1015 1_555 E C1 NAG . A NAG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale5 A ND2 ASN 1077 A ASN 1034 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.55 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? metalc ? metalc1 A OD1 ASP 418 A ASP 375 1_555 I NA NA . A NA 1609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc2 I NA NA . A NA 1609 1_555 J O HOH . A HOH 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? # _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 6A95 _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 E 4 NAG A 1 1605 1605 NAG NAG . F 4 NAG A 1 1606 1606 NAG NAG . G 4 NAG A 1 1607 1607 NAG NAG . H 5 9SR A 1 1608 1608 9SR 9SR . I 6 NA A 1 1609 1609 NA NA . J 7 HOH A 1 1701 1701 HOH HOH . # 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 . . . H 5 177.777 178.794 189.741 1 8.1 ? N12 9SR 1608 A 1 HETATM 2 C C13 9SR . . . H 5 176.88 178.456 188.675 1 8.1 ? C13 9SR 1608 A 1 HETATM 3 C C15 9SR . . . H 5 177.423 175.93 189.003 1 8.1 ? C15 9SR 1608 A 1 HETATM 4 C C17 9SR . . . H 5 177.826 176.365 190.384 1 8.1 ? C17 9SR 1608 A 1 HETATM 5 C C21 9SR . . . H 5 179.908 174.868 193.356 1 8.1 ? C21 9SR 1608 A 1 HETATM 6 C C02 9SR . . . H 5 179.452 177.177 192.625 1 8.1 ? C02 9SR 1608 A 1 HETATM 7 C C03 9SR . . . H 5 178.917 175.834 192.488 1 8.1 ? C03 9SR 1608 A 1 HETATM 8 C C05 9SR . . . H 5 178.842 175.432 191.086 1 8.1 ? C05 9SR 1608 A 1 HETATM 9 C C07 9SR . . . H 5 180.727 176.884 190.59 1 8.1 ? C07 9SR 1608 A 1 HETATM 10 C C09 9SR . . . H 5 179.977 177.891 189.852 1 8.1 ? C09 9SR 1608 A 1 HETATM 11 C C11 9SR . . . H 5 178.469 177.804 190.412 1 8.1 ? C11 9SR 1608 A 1 HETATM 12 C C19 9SR . . . H 5 178.524 178.183 191.919 1 8.1 ? C19 9SR 1608 A 1 HETATM 13 N N14 9SR . . . H 5 176.689 177.029 188.304 1 8.1 ? N14 9SR 1608 A 1 HETATM 14 N N18 9SR . . . H 5 176.212 179.496 187.951 1 8.1 ? N18 9SR 1608 A 1 HETATM 15 O O01 9SR . . . H 5 180.698 177.309 191.99 1 8.1 ? O01 9SR 1608 A 1 HETATM 16 O O04 9SR . . . H 5 177.641 175.815 193.038 1 8.1 ? O04 9SR 1608 A 1 HETATM 17 O O06 9SR . . . H 5 180.075 175.602 190.412 1 8.1 ? O06 9SR 1608 A 1 HETATM 18 O O08 9SR . . . H 5 182.039 176.818 190.166 1 8.1 ? O08 9SR 1608 A 1 HETATM 19 O O10 9SR . . . H 5 180.083 177.695 188.492 1 8.1 ? O10 9SR 1608 A 1 HETATM 20 O O16 9SR . . . H 5 176.626 174.803 189 1 8.1 ? O16 9SR 1608 A 1 HETATM 21 O O20 9SR . . . H 5 179.048 179.408 192.005 1 8.1 ? O20 9SR 1608 A 1 HETATM 22 O O22 9SR . . . H 5 179.752 173.555 192.938 1 8.1 ? O22 9SR 1608 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #