data_4XPT # _model_server_result.job_id D7tfDQpE4QrGzWLoWm2nEg _model_server_result.datetime_utc '2024-11-28 00:11:08' _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 4xpt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":612}' # _entry.id 4XPT # _exptl.entry_id 4XPT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 2 _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 4XPT _cell.length_a 96.614 _cell.length_b 139.148 _cell.length_c 166.679 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XPT _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 10 N N N ? 10 O N 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 GLC _pdbx_entity_branch_link.comp_id_2 BGC _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 BGC 1 B 1 BGC M 1 MAL 4 n D GLC 2 B 2 GLC M 1 MAL 4 n E BGC 1 C 1 BGC M 2 MAL 4 n E GLC 2 C 2 GLC M 2 MAL 4 n F BGC 1 D 1 BGC M 3 MAL 4 n F GLC 2 D 2 GLC M 3 MAL 4 n G BGC 1 E 1 BGC M 4 MAL 4 n G GLC 2 E 2 GLC M 4 MAL 4 n H BGC 1 F 1 BGC M 5 MAL 4 n H GLC 2 F 2 GLC M 5 MAL # 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 124 A CYS 148 1_555 A SG CYS 133 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 23 L CYS 23 1_555 B SG CYS 89 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 135 L CYS 135 1_555 B SG CYS 195 L CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 C SG CYS 146 H CYS 146 1_555 C SG CYS 201 H CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 117 A ASN 141 1_555 K C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 D O4 BGC . B BGC 1 1_555 D C1 GLC . B GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 sing covale ? covale3 E O4 BGC . C BGC 1 1_555 E C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 sing covale ? covale4 F O4 BGC . D BGC 1 1_555 F C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 sing covale ? covale5 G O4 BGC . E BGC 1 1_555 G C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 sing covale ? covale6 H O4 BGC . F BGC 1 1_555 H C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 sing metalc ? metalc1 A O GLY 18 A GLY 42 1_555 O NA NA . A NA 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc2 A O ALA 20 A ALA 44 1_555 N NA NA . A NA 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc3 A O VAL 21 A VAL 45 1_555 O NA NA . A NA 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc4 A OD1 ASP 22 A ASP 46 1_555 N NA NA . A NA 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc5 A OD1 ASN 25 A ASN 49 1_555 N NA NA . A NA 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc6 A O SER 256 A SER 320 1_555 N NA NA . A NA 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? metalc ? metalc7 A OG SER 256 A SER 320 1_555 N NA NA . A NA 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc8 A OD1 ASN 288 A ASN 352 1_555 N NA NA . A NA 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.063 ? metalc ? metalc9 A O LEU 353 A LEU 417 1_555 O NA NA . A NA 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc10 A OD1 ASP 356 A ASP 420 1_555 O NA NA . A NA 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc11 A OD2 ASP 356 A ASP 420 1_555 O NA NA . A NA 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? metalc ? metalc12 A OG SER 357 A SER 421 1_555 O NA NA . A NA 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? # _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 4XPT _atom_sites.fract_transf_matrix[1][1] 0.01035 _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] 0.007187 _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] 0.006 _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 I 5 Y01 A 1 601 1 Y01 CHS . J 6 42J A 1 602 601 42J DCP . K 7 NAG A 1 603 701 NAG NAG . L 8 CLR A 1 609 1 CLR CLR . M 9 CL A 1 610 1 CL CL . N 10 NA A 1 611 1 NA NA . O 10 NA A 1 612 2 NA NA . # _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 10 _atom_site.Cartn_x 98.602 _atom_site.Cartn_y 285.5 _atom_site.Cartn_z 25.962 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 91.26 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 612 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #