data_4XPB # _model_server_result.job_id CY6OnMl32et-MDo-Jh6YUA _model_server_result.datetime_utc '2024-10-14 11:24:53' _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 4xpb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":706}' # _entry.id 4XPB # _exptl.entry_id 4XPB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _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 4XPB _cell.length_a 97.498 _cell.length_b 139.963 _cell.length_c 166.959 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XPB _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 _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 ? 5 E N N ? 5 I 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 A 603 N9S 4 n D GLC 2 B 2 GLC A 603 N9S # 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 129 A CYS 148 1_555 A SG CYS 138 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 C SG CYS 41 H CYS 22 1_555 C SG CYS 115 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 C SG CYS 165 H CYS 146 1_555 C SG CYS 220 H CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 D O4 BGC . B BGC 1 1_555 D C1 GLC . B GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 sing metalc ? metalc1 A O GLY 23 A GLY 42 1_555 I NA NA . A NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc2 A O ALA 25 A ALA 44 1_555 E NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc3 A O VAL 26 A VAL 45 1_555 I NA NA . A NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc4 A OD1 ASN 30 A ASN 49 1_555 E NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc5 A O SER 258 A SER 320 1_555 E NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc6 A OG SER 258 A SER 320 1_555 E NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc7 A OD1 ASN 290 A ASN 352 1_555 E NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc8 A O LEU 355 A LEU 417 1_555 I NA NA . A NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc9 A OD1 ASP 358 A ASP 420 1_555 I NA NA . A NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc10 A OG SER 359 A SER 421 1_555 I NA NA . A NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc11 E NA NA . A NA 701 1_555 K O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? # _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 4XPB _atom_sites.fract_transf_matrix[1][1] 0.010257 _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] 0.007145 _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] 0.005989 _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 NA A 1 701 601 NA NA . F 6 COC A 1 702 602 COC COC . G 7 CLR A 1 704 604 CLR CLR . H 7 CLR A 1 705 605 CLR CLR . I 5 NA A 1 706 606 NA NA . J 8 CL A 1 707 607 CL CL . K 9 HOH A 1 801 701 HOH HOH . K 9 HOH A 2 802 702 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 I _atom_site.label_entity_id 5 _atom_site.Cartn_x -2.447 _atom_site.Cartn_y -5.947 _atom_site.Cartn_z 25.651 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 98.21 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 706 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #