data_5NDD # _model_server_result.job_id WkHoNvTGp-EuKWqf3KikOg _model_server_result.datetime_utc '2024-11-21 13:43:32' _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 5ndd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2202}' # _entry.id 5NDD # _exptl.entry_id 5NDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _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 104.88 _cell.angle_beta 90.88 _cell.angle_gamma 96.89 _cell.entry_id 5NDD _cell.length_a 37.109 _cell.length_b 62.264 _cell.length_c 87.341 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NDD _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 x,y,z _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 277 A CYS 148 1_555 A SG CYS 355 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A OD1 ASP 250 A ASP 121 1_555 C NA NA . A NA 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc2 A OD1 ASN 287 A ASN 158 1_555 C NA NA . A NA 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc3 A OG SER 291 A SER 162 1_555 C NA NA . A NA 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc4 A OD1 ASN 565 A ASN 336 1_555 C NA NA . A NA 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc5 A OD2 ASP 569 A ASP 340 1_555 C NA NA . A NA 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc6 C NA NA . A NA 2202 1_555 E O HOH . A HOH 2307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? # _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 5NDD _atom_sites.fract_transf_matrix[1][1] 0.026948 _atom_sites.fract_transf_matrix[1][2] 0.003257 _atom_sites.fract_transf_matrix[1][3] 0.001306 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016178 _atom_sites.fract_transf_matrix[2][3] 0.004365 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.01186 _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 B 2 8TZ A 1 2201 1 8TZ UNK . C 3 NA A 1 2202 1 NA NA . D 4 PO4 A 1 2203 1 PO4 PO4 . E 5 HOH A 1 2301 6 HOH HOH . E 5 HOH A 2 2302 7 HOH HOH . E 5 HOH A 3 2303 2 HOH HOH . E 5 HOH A 4 2304 1 HOH HOH . E 5 HOH A 5 2305 10 HOH HOH . E 5 HOH A 6 2306 8 HOH HOH . E 5 HOH A 7 2307 5 HOH HOH . E 5 HOH A 8 2308 9 HOH HOH . E 5 HOH A 9 2309 3 HOH HOH . E 5 HOH A 10 2310 4 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 C _atom_site.label_entity_id 3 _atom_site.Cartn_x 13.874 _atom_site.Cartn_y 5.728 _atom_site.Cartn_z 40.463 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 49.57 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 2202 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #