data_4X1D # _model_server_result.job_id qjAiYQmN00pIb3WEOF-cBQ _model_server_result.datetime_utc '2024-12-26 20:54:01' _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 4x1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":701}' # _entry.id 4X1D # _exptl.entry_id 4X1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 173.04 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'YTTERBIUM (III) 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 90.41 _cell.angle_gamma 90 _cell.entry_id 4X1D _cell.length_a 156.502 _cell.length_b 136.863 _cell.length_c 107.843 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 ? 2 C N N ? 2 F N 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 9 A CYS 9 1_555 A SG CYS 48 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? disulf ? disulf2 A SG CYS 19 A CYS 19 1_555 A SG CYS 39 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? disulf ? disulf3 A SG CYS 118 A CYS 118 1_555 A SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf4 A SG CYS 137 A CYS 137 1_555 A SG CYS 331 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? disulf ? disulf5 A SG CYS 158 A CYS 158 1_555 A SG CYS 174 A CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 A SG CYS 161 A CYS 161 1_555 A SG CYS 179 A CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf7 A SG CYS 171 A CYS 171 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf8 A SG CYS 227 A CYS 227 1_555 A SG CYS 241 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf9 A SG CYS 339 A CYS 339 1_555 A SG CYS 596 A CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf10 A SG CYS 345 A CYS 345 1_555 A SG CYS 377 A CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 A SG CYS 355 A CYS 355 1_555 A SG CYS 368 A CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf12 A SG CYS 402 A CYS 402 1_555 A SG CYS 674 A CYS 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf13 A SG CYS 450 A CYS 450 1_555 A SG CYS 523 A CYS 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf14 A SG CYS 474 A CYS 474 1_555 A SG CYS 665 A CYS 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf15 A SG CYS 484 A CYS 484 1_555 A SG CYS 498 A CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf16 A SG CYS 495 A CYS 495 1_555 A SG CYS 506 A CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf17 A SG CYS 563 A CYS 563 1_555 A SG CYS 577 A CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf18 B SG CYS 9 B CYS 9 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? disulf ? disulf19 B SG CYS 19 B CYS 19 1_555 B SG CYS 39 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? disulf ? disulf20 B SG CYS 118 B CYS 118 1_555 B SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? disulf ? disulf21 B SG CYS 137 B CYS 137 1_555 B SG CYS 331 B CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf22 B SG CYS 158 B CYS 158 1_555 B SG CYS 174 B CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf23 B SG CYS 161 B CYS 161 1_555 B SG CYS 179 B CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf24 B SG CYS 171 B CYS 171 1_555 B SG CYS 177 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf25 B SG CYS 227 B CYS 227 1_555 B SG CYS 241 B CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf26 B SG CYS 339 B CYS 339 1_555 B SG CYS 596 B CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf27 B SG CYS 345 B CYS 345 1_555 B SG CYS 377 B CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf28 B SG CYS 355 B CYS 355 1_555 B SG CYS 368 B CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf29 B SG CYS 402 B CYS 402 1_555 B SG CYS 674 B CYS 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf30 B SG CYS 450 B CYS 450 1_555 B SG CYS 523 B CYS 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf31 B SG CYS 474 B CYS 474 1_555 B SG CYS 665 B CYS 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf32 B SG CYS 484 B CYS 484 1_555 B SG CYS 498 B CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf33 B SG CYS 495 B CYS 495 1_555 B SG CYS 506 B CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf34 B SG CYS 563 B CYS 563 1_555 B SG CYS 577 B CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc1 A OD1 ASP 392 A ASP 392 1_555 C YB YB . A YB 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc2 A OH TYR 426 A TYR 426 1_555 C YB YB . A YB 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc3 A OH TYR 517 A TYR 517 1_555 C YB YB . A YB 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc4 A NE2 HIS 585 A HIS 585 1_555 C YB YB . A YB 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc5 C YB YB . A YB 701 1_555 D O7 MLI . A MLI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc6 C YB YB . A YB 701 1_555 D O9 MLI . A MLI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc7 B OD1 ASP 392 B ASP 392 1_555 F YB YB . B YB 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc8 B OH TYR 426 B TYR 426 1_555 F YB YB . B YB 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc9 B OH TYR 517 B TYR 517 1_555 F YB YB . B YB 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc10 B NE2 HIS 585 B HIS 585 1_555 F YB YB . B YB 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc11 F YB YB . B YB 701 1_555 G O9 MLI . B MLI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc12 F YB YB . B YB 701 1_555 G O7 MLI . B MLI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? # _chem_comp.formula 'Yb 3' _chem_comp.formula_weight 173.04 _chem_comp.id YB _chem_comp.mon_nstd_flag . _chem_comp.name 'YTTERBIUM (III) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4X1D _atom_sites.fract_transf_matrix[1][1] 0.00639 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000046 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007307 _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] 0.009273 _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 C 2 YB A 1 701 680 YB YB . D 3 MLI A 1 702 681 MLI MLI . E 4 GOL A 1 703 682 GOL GOL . F 2 YB B 1 701 680 YB YB . G 3 MLI B 1 702 681 MLI MLI . H 4 GOL B 1 703 682 GOL GOL . I 5 HOH A 1 801 48 HOH HOH . I 5 HOH A 2 802 25 HOH HOH . I 5 HOH A 3 803 103 HOH HOH . I 5 HOH A 4 804 113 HOH HOH . I 5 HOH A 5 805 12 HOH HOH . I 5 HOH A 6 806 33 HOH HOH . I 5 HOH A 7 807 31 HOH HOH . I 5 HOH A 8 808 66 HOH HOH . I 5 HOH A 9 809 92 HOH HOH . I 5 HOH A 10 810 132 HOH HOH . I 5 HOH A 11 811 81 HOH HOH . I 5 HOH A 12 812 100 HOH HOH . I 5 HOH A 13 813 101 HOH HOH . I 5 HOH A 14 814 123 HOH HOH . I 5 HOH A 15 815 109 HOH HOH . I 5 HOH A 16 816 118 HOH HOH . I 5 HOH A 17 817 120 HOH HOH . I 5 HOH A 18 818 127 HOH HOH . I 5 HOH A 19 819 2 HOH HOH . I 5 HOH A 20 820 4 HOH HOH . I 5 HOH A 21 821 6 HOH HOH . I 5 HOH A 22 822 7 HOH HOH . I 5 HOH A 23 823 13 HOH HOH . I 5 HOH A 24 824 15 HOH HOH . I 5 HOH A 25 825 16 HOH HOH . I 5 HOH A 26 826 18 HOH HOH . I 5 HOH A 27 827 21 HOH HOH . I 5 HOH A 28 828 22 HOH HOH . I 5 HOH A 29 829 23 HOH HOH . I 5 HOH A 30 830 24 HOH HOH . I 5 HOH A 31 831 26 HOH HOH . I 5 HOH A 32 832 28 HOH HOH . I 5 HOH A 33 833 29 HOH HOH . I 5 HOH A 34 834 30 HOH HOH . I 5 HOH A 35 835 32 HOH HOH . I 5 HOH A 36 836 34 HOH HOH . I 5 HOH A 37 837 36 HOH HOH . I 5 HOH A 38 838 38 HOH HOH . I 5 HOH A 39 839 40 HOH HOH . I 5 HOH A 40 840 42 HOH HOH . I 5 HOH A 41 841 43 HOH HOH . I 5 HOH A 42 842 44 HOH HOH . I 5 HOH A 43 843 47 HOH HOH . I 5 HOH A 44 844 50 HOH HOH . I 5 HOH A 45 845 57 HOH HOH . I 5 HOH A 46 846 59 HOH HOH . I 5 HOH A 47 847 62 HOH HOH . I 5 HOH A 48 848 63 HOH HOH . I 5 HOH A 49 849 64 HOH HOH . I 5 HOH A 50 850 67 HOH HOH . I 5 HOH A 51 851 68 HOH HOH . I 5 HOH A 52 852 69 HOH HOH . I 5 HOH A 53 853 71 HOH HOH . I 5 HOH A 54 854 74 HOH HOH . I 5 HOH A 55 855 75 HOH HOH . I 5 HOH A 56 856 77 HOH HOH . I 5 HOH A 57 857 79 HOH HOH . I 5 HOH A 58 858 80 HOH HOH . I 5 HOH A 59 859 83 HOH HOH . I 5 HOH A 60 860 86 HOH HOH . I 5 HOH A 61 861 89 HOH HOH . I 5 HOH A 62 862 91 HOH HOH . I 5 HOH A 63 863 94 HOH HOH . I 5 HOH A 64 864 102 HOH HOH . I 5 HOH A 65 865 105 HOH HOH . I 5 HOH A 66 866 106 HOH HOH . I 5 HOH A 67 867 108 HOH HOH . I 5 HOH A 68 868 114 HOH HOH . I 5 HOH A 69 869 115 HOH HOH . I 5 HOH A 70 870 116 HOH HOH . I 5 HOH A 71 871 119 HOH HOH . I 5 HOH A 72 872 122 HOH HOH . I 5 HOH A 73 873 124 HOH HOH . I 5 HOH A 74 874 126 HOH HOH . I 5 HOH A 75 875 128 HOH HOH . I 5 HOH A 76 876 131 HOH HOH . I 5 HOH A 77 877 134 HOH HOH . I 5 HOH A 78 878 138 HOH HOH . J 5 HOH B 1 801 65 HOH HOH . J 5 HOH B 2 802 121 HOH HOH . J 5 HOH B 3 803 14 HOH HOH . J 5 HOH B 4 804 73 HOH HOH . J 5 HOH B 5 805 76 HOH HOH . J 5 HOH B 6 806 39 HOH HOH . J 5 HOH B 7 807 35 HOH HOH . J 5 HOH B 8 808 96 HOH HOH . J 5 HOH B 9 809 84 HOH HOH . J 5 HOH B 10 810 104 HOH HOH . J 5 HOH B 11 811 82 HOH HOH . J 5 HOH B 12 812 1 HOH HOH . J 5 HOH B 13 813 3 HOH HOH . J 5 HOH B 14 814 5 HOH HOH . J 5 HOH B 15 815 8 HOH HOH . J 5 HOH B 16 816 9 HOH HOH . J 5 HOH B 17 817 10 HOH HOH . J 5 HOH B 18 818 11 HOH HOH . J 5 HOH B 19 819 17 HOH HOH . J 5 HOH B 20 820 19 HOH HOH . J 5 HOH B 21 821 20 HOH HOH . J 5 HOH B 22 822 27 HOH HOH . J 5 HOH B 23 823 37 HOH HOH . J 5 HOH B 24 824 41 HOH HOH . J 5 HOH B 25 825 45 HOH HOH . J 5 HOH B 26 826 46 HOH HOH . J 5 HOH B 27 827 49 HOH HOH . J 5 HOH B 28 828 51 HOH HOH . J 5 HOH B 29 829 52 HOH HOH . J 5 HOH B 30 830 53 HOH HOH . J 5 HOH B 31 831 54 HOH HOH . J 5 HOH B 32 832 55 HOH HOH . J 5 HOH B 33 833 56 HOH HOH . J 5 HOH B 34 834 58 HOH HOH . J 5 HOH B 35 835 60 HOH HOH . J 5 HOH B 36 836 61 HOH HOH . J 5 HOH B 37 837 70 HOH HOH . J 5 HOH B 38 838 72 HOH HOH . J 5 HOH B 39 839 78 HOH HOH . J 5 HOH B 40 840 85 HOH HOH . J 5 HOH B 41 841 87 HOH HOH . J 5 HOH B 42 842 88 HOH HOH . J 5 HOH B 43 843 90 HOH HOH . J 5 HOH B 44 844 93 HOH HOH . J 5 HOH B 45 845 95 HOH HOH . J 5 HOH B 46 846 97 HOH HOH . J 5 HOH B 47 847 98 HOH HOH . J 5 HOH B 48 848 99 HOH HOH . J 5 HOH B 49 849 107 HOH HOH . J 5 HOH B 50 850 110 HOH HOH . J 5 HOH B 51 851 111 HOH HOH . J 5 HOH B 52 852 112 HOH HOH . J 5 HOH B 53 853 117 HOH HOH . J 5 HOH B 54 854 125 HOH HOH . J 5 HOH B 55 855 129 HOH HOH . J 5 HOH B 56 856 130 HOH HOH . J 5 HOH B 57 857 133 HOH HOH . J 5 HOH B 58 858 135 HOH HOH . J 5 HOH B 59 859 136 HOH HOH . J 5 HOH B 60 860 137 HOH HOH . J 5 HOH B 61 861 139 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol YB _atom_site.label_atom_id YB _atom_site.label_comp_id YB _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id F _atom_site.label_entity_id 2 _atom_site.Cartn_x -29.688 _atom_site.Cartn_y -35.774 _atom_site.Cartn_z 50.036 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 47.54 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id YB _atom_site.auth_comp_id YB _atom_site.auth_seq_id 701 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #