data_5VLK # _model_server_result.job_id yfHD874xbH1pu3kLf86DLg _model_server_result.datetime_utc '2025-07-07 19:35:17' _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 5vlk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5VLK # _exptl.entry_id 5VLK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM 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 120 _cell.entry_id 5VLK _cell.length_a 70.387 _cell.length_b 70.387 _cell.length_c 156.983 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VLK _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G _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 4 _struct_asym.id D _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 223 A CYS 223 1_555 A SG CYS 255 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 A SG CYS 323 A CYS 323 1_555 A SG CYS 358 A CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf3 A SG CYS 375 A CYS 375 1_555 A SG CYS 378 A CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 B C ACE 1 Y ACE 0 1_555 B N THR 2 Y THR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale2 B C VAL 14 Y VAL 13 1_555 B N NH2 15 Y NH2 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.281 ? covale ? covale3 C C ACE 1 Z ACE 0 1_555 C N TRP 2 Z TRP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale4 C C VAL 5 Z VAL 4 1_555 C N HRG 6 Z HRG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 C C HRG 6 Z HRG 5 1_555 C N ILE 7 Z ILE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? metalc ? metalc1 A O PRO 331 A PRO 331 1_555 D CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 A O VAL 333 A VAL 333 1_555 D CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc3 A OD1 ASP 360 A ASP 360 1_555 D CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? metalc ? metalc4 A OD2 ASP 360 A ASP 360 1_555 D CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc5 D CA CA . A CA 501 1_555 E O HOH . A HOH 651 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc6 D CA CA . A CA 501 1_555 E O HOH . A HOH 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc7 D CA CA . A CA 501 1_555 E O HOH . A HOH 753 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5VLK _atom_sites.fract_transf_matrix[1][1] 0.014207 _atom_sites.fract_transf_matrix[1][2] 0.008203 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016405 _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] 0.00637 _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 D 4 CA A 1 501 1 CA CA . E 5 HOH A 1 601 27 HOH HOH . E 5 HOH A 2 602 160 HOH HOH . E 5 HOH A 3 603 182 HOH HOH . E 5 HOH A 4 604 24 HOH HOH . E 5 HOH A 5 605 39 HOH HOH . E 5 HOH A 6 606 161 HOH HOH . E 5 HOH A 7 607 145 HOH HOH . E 5 HOH A 8 608 77 HOH HOH . E 5 HOH A 9 609 144 HOH HOH . E 5 HOH A 10 610 18 HOH HOH . E 5 HOH A 11 611 68 HOH HOH . E 5 HOH A 12 612 14 HOH HOH . E 5 HOH A 13 613 163 HOH HOH . E 5 HOH A 14 614 95 HOH HOH . E 5 HOH A 15 615 166 HOH HOH . E 5 HOH A 16 616 214 HOH HOH . E 5 HOH A 17 617 152 HOH HOH . E 5 HOH A 18 618 25 HOH HOH . E 5 HOH A 19 619 52 HOH HOH . E 5 HOH A 20 620 3 HOH HOH . E 5 HOH A 21 621 41 HOH HOH . E 5 HOH A 22 622 120 HOH HOH . E 5 HOH A 23 623 207 HOH HOH . E 5 HOH A 24 624 2 HOH HOH . E 5 HOH A 25 625 146 HOH HOH . E 5 HOH A 26 626 111 HOH HOH . E 5 HOH A 27 627 93 HOH HOH . E 5 HOH A 28 628 212 HOH HOH . E 5 HOH A 29 629 202 HOH HOH . E 5 HOH A 30 630 53 HOH HOH . E 5 HOH A 31 631 183 HOH HOH . E 5 HOH A 32 632 32 HOH HOH . E 5 HOH A 33 633 61 HOH HOH . E 5 HOH A 34 634 17 HOH HOH . E 5 HOH A 35 635 99 HOH HOH . E 5 HOH A 36 636 135 HOH HOH . E 5 HOH A 37 637 87 HOH HOH . E 5 HOH A 38 638 26 HOH HOH . E 5 HOH A 39 639 10 HOH HOH . E 5 HOH A 40 640 121 HOH HOH . E 5 HOH A 41 641 8 HOH HOH . E 5 HOH A 42 642 37 HOH HOH . E 5 HOH A 43 643 57 HOH HOH . E 5 HOH A 44 644 4 HOH HOH . E 5 HOH A 45 645 155 HOH HOH . E 5 HOH A 46 646 33 HOH HOH . E 5 HOH A 47 647 7 HOH HOH . E 5 HOH A 48 648 156 HOH HOH . E 5 HOH A 49 649 13 HOH HOH . E 5 HOH A 50 650 75 HOH HOH . E 5 HOH A 51 651 11 HOH HOH . E 5 HOH A 52 652 29 HOH HOH . E 5 HOH A 53 653 149 HOH HOH . E 5 HOH A 54 654 62 HOH HOH . E 5 HOH A 55 655 48 HOH HOH . E 5 HOH A 56 656 22 HOH HOH . E 5 HOH A 57 657 58 HOH HOH . E 5 HOH A 58 658 217 HOH HOH . E 5 HOH A 59 659 28 HOH HOH . E 5 HOH A 60 660 71 HOH HOH . E 5 HOH A 61 661 170 HOH HOH . E 5 HOH A 62 662 74 HOH HOH . E 5 HOH A 63 663 44 HOH HOH . E 5 HOH A 64 664 54 HOH HOH . E 5 HOH A 65 665 124 HOH HOH . E 5 HOH A 66 666 127 HOH HOH . E 5 HOH A 67 667 82 HOH HOH . E 5 HOH A 68 668 36 HOH HOH . E 5 HOH A 69 669 200 HOH HOH . E 5 HOH A 70 670 5 HOH HOH . E 5 HOH A 71 671 137 HOH HOH . E 5 HOH A 72 672 89 HOH HOH . E 5 HOH A 73 673 56 HOH HOH . E 5 HOH A 74 674 45 HOH HOH . E 5 HOH A 75 675 197 HOH HOH . E 5 HOH A 76 676 198 HOH HOH . E 5 HOH A 77 677 34 HOH HOH . E 5 HOH A 78 678 47 HOH HOH . E 5 HOH A 79 679 102 HOH HOH . E 5 HOH A 80 680 169 HOH HOH . E 5 HOH A 81 681 105 HOH HOH . E 5 HOH A 82 682 116 HOH HOH . E 5 HOH A 83 683 84 HOH HOH . E 5 HOH A 84 684 167 HOH HOH . E 5 HOH A 85 685 60 HOH HOH . E 5 HOH A 86 686 63 HOH HOH . E 5 HOH A 87 687 76 HOH HOH . E 5 HOH A 88 688 140 HOH HOH . E 5 HOH A 89 689 35 HOH HOH . E 5 HOH A 90 690 73 HOH HOH . E 5 HOH A 91 691 42 HOH HOH . E 5 HOH A 92 692 66 HOH HOH . E 5 HOH A 93 693 79 HOH HOH . E 5 HOH A 94 694 81 HOH HOH . E 5 HOH A 95 695 12 HOH HOH . E 5 HOH A 96 696 117 HOH HOH . E 5 HOH A 97 697 136 HOH HOH . E 5 HOH A 98 698 70 HOH HOH . E 5 HOH A 99 699 9 HOH HOH . E 5 HOH A 100 700 23 HOH HOH . E 5 HOH A 101 701 205 HOH HOH . E 5 HOH A 102 702 112 HOH HOH . E 5 HOH A 103 703 15 HOH HOH . E 5 HOH A 104 704 40 HOH HOH . E 5 HOH A 105 705 194 HOH HOH . E 5 HOH A 106 706 80 HOH HOH . E 5 HOH A 107 707 131 HOH HOH . E 5 HOH A 108 708 108 HOH HOH . E 5 HOH A 109 709 1 HOH HOH . E 5 HOH A 110 710 59 HOH HOH . E 5 HOH A 111 711 46 HOH HOH . E 5 HOH A 112 712 176 HOH HOH . E 5 HOH A 113 713 51 HOH HOH . E 5 HOH A 114 714 21 HOH HOH . E 5 HOH A 115 715 151 HOH HOH . E 5 HOH A 116 716 90 HOH HOH . E 5 HOH A 117 717 38 HOH HOH . E 5 HOH A 118 718 30 HOH HOH . E 5 HOH A 119 719 122 HOH HOH . E 5 HOH A 120 720 6 HOH HOH . E 5 HOH A 121 721 164 HOH HOH . E 5 HOH A 122 722 88 HOH HOH . E 5 HOH A 123 723 69 HOH HOH . E 5 HOH A 124 724 177 HOH HOH . E 5 HOH A 125 725 114 HOH HOH . E 5 HOH A 126 726 43 HOH HOH . E 5 HOH A 127 727 172 HOH HOH . E 5 HOH A 128 728 98 HOH HOH . E 5 HOH A 129 729 189 HOH HOH . E 5 HOH A 130 730 96 HOH HOH . E 5 HOH A 131 731 119 HOH HOH . E 5 HOH A 132 732 219 HOH HOH . E 5 HOH A 133 733 86 HOH HOH . E 5 HOH A 134 734 201 HOH HOH . E 5 HOH A 135 735 19 HOH HOH . E 5 HOH A 136 736 123 HOH HOH . E 5 HOH A 137 737 101 HOH HOH . E 5 HOH A 138 738 92 HOH HOH . E 5 HOH A 139 739 31 HOH HOH . E 5 HOH A 140 740 109 HOH HOH . E 5 HOH A 141 741 203 HOH HOH . E 5 HOH A 142 742 94 HOH HOH . E 5 HOH A 143 743 72 HOH HOH . E 5 HOH A 144 744 83 HOH HOH . E 5 HOH A 145 745 196 HOH HOH . E 5 HOH A 146 746 139 HOH HOH . E 5 HOH A 147 747 186 HOH HOH . E 5 HOH A 148 748 130 HOH HOH . E 5 HOH A 149 749 150 HOH HOH . E 5 HOH A 150 750 20 HOH HOH . E 5 HOH A 151 751 49 HOH HOH . E 5 HOH A 152 752 193 HOH HOH . E 5 HOH A 153 753 78 HOH HOH . E 5 HOH A 154 754 113 HOH HOH . E 5 HOH A 155 755 106 HOH HOH . E 5 HOH A 156 756 65 HOH HOH . E 5 HOH A 157 757 85 HOH HOH . E 5 HOH A 158 758 181 HOH HOH . E 5 HOH A 159 759 50 HOH HOH . E 5 HOH A 160 760 221 HOH HOH . E 5 HOH A 161 761 191 HOH HOH . E 5 HOH A 162 762 179 HOH HOH . E 5 HOH A 163 763 154 HOH HOH . E 5 HOH A 164 764 133 HOH HOH . E 5 HOH A 165 765 16 HOH HOH . E 5 HOH A 166 766 162 HOH HOH . E 5 HOH A 167 767 128 HOH HOH . E 5 HOH A 168 768 91 HOH HOH . E 5 HOH A 169 769 118 HOH HOH . E 5 HOH A 170 770 138 HOH HOH . E 5 HOH A 171 771 199 HOH HOH . E 5 HOH A 172 772 216 HOH HOH . E 5 HOH A 173 773 208 HOH HOH . E 5 HOH A 174 774 210 HOH HOH . E 5 HOH A 175 775 110 HOH HOH . E 5 HOH A 176 776 147 HOH HOH . E 5 HOH A 177 777 157 HOH HOH . E 5 HOH A 178 778 185 HOH HOH . E 5 HOH A 179 779 100 HOH HOH . E 5 HOH A 180 780 126 HOH HOH . E 5 HOH A 181 781 153 HOH HOH . E 5 HOH A 182 782 104 HOH HOH . E 5 HOH A 183 783 171 HOH HOH . E 5 HOH A 184 784 175 HOH HOH . E 5 HOH A 185 785 168 HOH HOH . E 5 HOH A 186 786 173 HOH HOH . E 5 HOH A 187 787 64 HOH HOH . E 5 HOH A 188 788 206 HOH HOH . E 5 HOH A 189 789 103 HOH HOH . E 5 HOH A 190 790 165 HOH HOH . E 5 HOH A 191 791 141 HOH HOH . E 5 HOH A 192 792 211 HOH HOH . E 5 HOH A 193 793 218 HOH HOH . E 5 HOH A 194 794 215 HOH HOH . E 5 HOH A 195 795 180 HOH HOH . E 5 HOH A 196 796 67 HOH HOH . E 5 HOH A 197 797 184 HOH HOH . E 5 HOH A 198 798 174 HOH HOH . E 5 HOH A 199 799 178 HOH HOH . F 5 HOH Y 1 201 134 HOH HOH . F 5 HOH Y 2 202 220 HOH HOH . F 5 HOH Y 3 203 107 HOH HOH . F 5 HOH Y 4 204 132 HOH HOH . F 5 HOH Y 5 205 115 HOH HOH . F 5 HOH Y 6 206 142 HOH HOH . F 5 HOH Y 7 207 125 HOH HOH . F 5 HOH Y 8 208 97 HOH HOH . F 5 HOH Y 9 209 187 HOH HOH . F 5 HOH Y 10 210 190 HOH HOH . G 5 HOH Z 1 101 55 HOH HOH . G 5 HOH Z 2 102 213 HOH HOH . G 5 HOH Z 3 103 192 HOH HOH . G 5 HOH Z 4 104 188 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x 12.52 _atom_site.Cartn_y -13.692 _atom_site.Cartn_z 0.193 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 41.69 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 501 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 1 #