data_6J8I # _model_server_result.job_id Stro93P37LrmlixGC77nEQ _model_server_result.datetime_utc '2024-12-23 09:58:56' _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 6j8i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":2007}' # _entry.id 6J8I # _exptl.entry_id 6J8I _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 319.268 _entity.id 6 _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 6J8I _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6J8I _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 _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 6 _struct_asym.id I _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 D 1 NAG A 1901 NAG 4 n D NAG 2 D 2 NAG A 1902 NAG 4 n E NAG 1 E 1 NAG A 1903 NAG 4 n E NAG 2 E 2 NAG A 1904 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 50 C CYS 50 1_555 A SG CYS 127 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? disulf ? disulf2 A SG CYS 55 C CYS 55 1_555 B SG CYS 938 A CYS 895 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? disulf ? disulf3 A SG CYS 72 C CYS 72 1_555 A SG CYS 75 C CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf4 B SG CYS 318 A CYS 275 1_555 B SG CYS 358 A CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? disulf ? disulf5 B SG CYS 940 A CYS 897 1_555 B SG CYS 946 A CYS 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 B SG CYS 978 A CYS 935 1_555 B SG CYS 987 A CYS 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? disulf ? disulf7 B SG CYS 1393 A CYS 1350 1_555 B SG CYS 1413 A CYS 1370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf8 B SG CYS 1758 A CYS 1715 1_555 B SG CYS 1773 A CYS 1730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? disulf ? disulf9 C SG CYS 21 B CYS 21 1_555 C SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf10 C SG CYS 40 B CYS 40 1_555 C SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? covale ? covale1 A ND2 ASN 66 C ASN 66 1_555 F C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale2 B ND2 ASN 326 A ASN 283 1_555 H C1 NAG . A NAG 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? covale ? covale3 B ND2 ASN 1395 A ASN 1352 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.486 ? covale ? covale4 B ND2 ASN 1409 A ASN 1366 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? covale ? covale5 B ND2 ASN 1418 A ASN 1375 1_555 G C1 NAG . A NAG 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.515 ? covale ? covale6 C ND2 ASN 93 B ASN 93 1_555 J C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? covale ? covale7 C ND2 ASN 110 B ASN 110 1_555 K C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.526 ? covale ? covale8 C ND2 ASN 114 B ASN 114 1_555 L C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.527 ? covale ? covale9 C ND2 ASN 135 B ASN 135 1_555 M C1 NAG . B NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 6J8I _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 NAG C 1 301 301 NAG NAG . G 5 NAG A 1 2005 1905 NAG NAG . H 5 NAG A 1 2006 1906 NAG NAG . I 6 9SR A 1 2007 1 9SR LIG . J 5 NAG B 1 301 301 NAG NAG . K 5 NAG B 1 302 302 NAG NAG . L 5 NAG B 1 303 303 NAG NAG . M 5 NAG B 1 304 304 NAG NAG . # 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 . . . I 6 135.945 134.807 143.128 1 44.54 ? N12 9SR 2007 A 1 HETATM 2 C C13 9SR . . . I 6 135.091 134.322 142.067 1 44.54 ? C13 9SR 2007 A 1 HETATM 3 C C15 9SR . . . I 6 135.799 131.928 142.688 1 44.54 ? C15 9SR 2007 A 1 HETATM 4 C C17 9SR . . . I 6 136.06 132.508 144.037 1 44.54 ? C17 9SR 2007 A 1 HETATM 5 C C21 9SR . . . I 6 138.13 131.124 146.98 1 44.54 ? C21 9SR 2007 A 1 HETATM 6 C C02 9SR . . . I 6 137.774 133.455 146.113 1 44.54 ? C02 9SR 2007 A 1 HETATM 7 C C03 9SR . . . I 6 137.172 132.134 146.139 1 44.54 ? C03 9SR 2007 A 1 HETATM 8 C C05 9SR . . . I 6 137.036 131.612 144.795 1 44.54 ? C05 9SR 2007 A 1 HETATM 9 C C07 9SR . . . I 6 138.919 132.942 144.064 1 44.54 ? C07 9SR 2007 A 1 HETATM 10 C C09 9SR . . . I 6 138.125 133.826 143.258 1 44.54 ? C09 9SR 2007 A 1 HETATM 11 C C11 9SR . . . I 6 136.688 133.916 143.905 1 44.54 ? C11 9SR 2007 A 1 HETATM 12 C C19 9SR . . . I 6 136.866 134.442 145.353 1 44.54 ? C19 9SR 2007 A 1 HETATM 13 N N14 9SR . . . I 6 134.992 132.846 141.824 1 44.54 ? N14 9SR 2007 A 1 HETATM 14 N N18 9SR . . . I 6 134.327 135.247 141.26 1 44.54 ? N18 9SR 2007 A 1 HETATM 15 O O01 9SR . . . I 6 138.992 133.48 145.426 1 44.54 ? O01 9SR 2007 A 1 HETATM 16 O O04 9SR . . . I 6 135.936 132.171 146.764 1 44.54 ? O04 9SR 2007 A 1 HETATM 17 O O06 9SR . . . I 6 138.236 131.675 144.054 1 44.54 ? O06 9SR 2007 A 1 HETATM 18 O O08 9SR . . . I 6 140.173 132.839 143.483 1 44.54 ? O08 9SR 2007 A 1 HETATM 19 O O10 9SR . . . I 6 138.063 133.241 142.011 1 44.54 ? O10 9SR 2007 A 1 HETATM 20 O O16 9SR . . . I 6 135.084 130.76 142.902 1 44.54 ? O16 9SR 2007 A 1 HETATM 21 O O20 9SR . . . I 6 137.489 135.636 145.276 1 44.54 ? O20 9SR 2007 A 1 HETATM 22 O O22 9SR . . . I 6 139.384 131.118 146.37 1 44.54 ? O22 9SR 2007 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 22 #