data_8FD7 # _model_server_result.job_id 2SJbbjg_DDeFztrPTfiUtA _model_server_result.datetime_utc '2024-11-04 22:37:52' _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 8fd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1211}' # _entry.id 8FD7 # _exptl.entry_id 8FD7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 22.99 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 8FD7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FD7 _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,T,U,V,W _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 8 _struct_asym.id O _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 F 1 NAG F 2 NAG 4 n D NAG 2 F 2 NAG F 1 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 305 D CYS 305 1_555 A SG CYS 1046 D CYS 1046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 356 D CYS 356 1_555 A SG CYS 1061 D CYS 1061 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 406 D CYS 406 1_555 A SG CYS 1073 D CYS 1073 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 669 D CYS 669 1_555 A SG CYS 699 D CYS 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 906 D CYS 906 1_555 A SG CYS 976 D CYS 976 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 998 D CYS 998 1_555 A SG CYS 1028 D CYS 1028 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 1001 D CYS 1001 1_555 A SG CYS 1026 D CYS 1026 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 316 K CYS 316 1_555 B SG CYS 332 K CYS 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 1058 K CYS 1058 1_555 B SG CYS 1069 K CYS 1069 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 B SG CYS 1431 K CYS 1431 1_555 B SG CYS 1447 K CYS 1447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 94 D ASN 94 1_555 G C1 NAG . D NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 470 D ASN 470 1_555 H C1 NAG . D NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 D O4 NAG . F NAG 1 1_555 D C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A OG SER 263 D SER 263 1_555 N CA CA . D CA 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc2 A OG SER 265 D SER 265 1_555 N CA CA . D CA 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc3 A OG1 THR 333 D THR 333 1_555 N CA CA . D CA 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc4 A O TRP 448 D TRP 448 1_555 O NA NA . D NA 1211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc5 B OE1 GLU 363 K GLU 363 1_555 V CA CA . K CA 1707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 B OE2 GLU 363 K GLU 363 1_555 V CA CA . K CA 1707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.185 ? metalc ? metalc7 B OE2 GLU 1115 K GLU 1115 1_555 V CA CA . K CA 1707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.048 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 8FD7 _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 5 NAG D 1 1201 1103 NAG NAG . F 6 GBN D 1 1202 1116 GBN GBN . G 5 NAG D 1 1203 1117 NAG NAG . H 5 NAG D 1 1204 1118 NAG NAG . I 5 NAG D 1 1205 1119 NAG NAG . J 5 NAG D 1 1206 1120 NAG NAG . K 5 NAG D 1 1207 3 NAG NAG . L 5 NAG D 1 1208 4 NAG NAG . M 5 NAG D 1 1209 5 NAG NAG . N 7 CA D 1 1210 1 CA CA . O 8 NA D 1 1211 1 NA NA . P 9 WO9 K 1 1701 1710 WO9 WO9 . Q 10 YSW K 1 1702 1711 YSW WNZ . R 11 CLR K 1 1703 1712 CLR CLR . S 11 CLR K 1 1704 1713 CLR CLR . T 11 CLR K 1 1705 1714 CLR CLR . U 7 CA K 1 1706 3 CA CA . V 7 CA K 1 1707 4 CA CA . W 12 HOH K 1 1801 1 HOH HOH . W 12 HOH K 2 1802 3 HOH HOH . W 12 HOH K 3 1803 2 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id O _atom_site.label_entity_id 8 _atom_site.Cartn_x 182.665 _atom_site.Cartn_y 168.27 _atom_site.Cartn_z 131.683 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 30 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1211 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #