data_7BYV # _model_server_result.job_id 9N9Xr03WYKRV4HWYPSXjfA _model_server_result.datetime_utc '2024-12-26 19:16:53' _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 7byv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":506}' # _entry.id 7BYV # _exptl.entry_id 7BYV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 5 _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 111.328 _cell.angle_gamma 90 _cell.entry_id 7BYV _cell.length_a 66.08 _cell.length_b 50.412 _cell.length_c 75.698 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BYV _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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,F,G,H _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 GAL GAL C1 O1 . O3 HO3 . sing 4 ? 3 3 2 GAL GAL C1 O1 . O3 HO3 . 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 2 n B NAG 1 B 1 NAG A 505 NAG 2 n B NAG 2 B 2 NAG A 504 NAG 2 n B BMA 3 B 3 BMA A 503 BMA 3 n C GAL 1 C 1 GAL A 509 GAL 3 n C GAL 2 C 2 GAL A 508 GAL 3 n C GAL 3 C 3 GAL A 507 GAL # 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 51 A CYS 71 1_555 A SG CYS 120 A CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? covale ? covale1 A ND2 ASN 59 A ASN 79 1_555 D C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 174 A ASN 194 1_555 E C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 A ND2 ASN 369 A ASN 389 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale6 C O3 GAL . C GAL 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale7 C O3 GAL . C GAL 2 1_555 C C1 GAL . C GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? metalc ? metalc1 A OE1 GLU 309 A GLU 329 1_555 F CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc2 A OE1 GLU 311 A GLU 331 1_555 F CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc3 A OE2 GLU 311 A GLU 331 1_555 F CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc4 A O SER 328 A SER 348 1_555 F CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc5 A O LYS 331 A LYS 351 1_555 F CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc6 A O ASP 423 A ASP 443 1_555 F CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc7 A OD1 ASP 423 A ASP 443 1_555 F CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? # _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 7BYV _atom_sites.fract_transf_matrix[1][1] 0.015133 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005909 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019837 _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] 0.014182 _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 NAG A 1 501 501 NAG NAG . E 4 NAG A 1 502 502 NAG NAG . F 5 CA A 1 506 506 CA CA . G 6 GAL A 1 510 510 GAL GAL . H 7 HOH A 1 601 601 HOH HOH . H 7 HOH A 2 602 604 HOH HOH . H 7 HOH A 3 603 602 HOH HOH . H 7 HOH A 4 604 603 HOH HOH . H 7 HOH A 5 605 606 HOH HOH . H 7 HOH A 6 606 605 HOH HOH . H 7 HOH A 7 607 607 HOH HOH . H 7 HOH A 8 608 610 HOH HOH . H 7 HOH A 9 609 608 HOH HOH . H 7 HOH A 10 610 609 HOH HOH . H 7 HOH A 11 611 611 HOH HOH . H 7 HOH A 12 612 612 HOH HOH . H 7 HOH A 13 613 614 HOH HOH . H 7 HOH A 14 614 613 HOH HOH . H 7 HOH A 15 615 616 HOH HOH . H 7 HOH A 16 616 621 HOH HOH . H 7 HOH A 17 617 618 HOH HOH . H 7 HOH A 18 618 615 HOH HOH . H 7 HOH A 19 619 620 HOH HOH . H 7 HOH A 20 620 617 HOH HOH . H 7 HOH A 21 621 622 HOH HOH . H 7 HOH A 22 622 623 HOH HOH . H 7 HOH A 23 623 630 HOH HOH . H 7 HOH A 24 624 624 HOH HOH . H 7 HOH A 25 625 619 HOH HOH . H 7 HOH A 26 626 626 HOH HOH . H 7 HOH A 27 627 632 HOH HOH . H 7 HOH A 28 628 628 HOH HOH . H 7 HOH A 29 629 631 HOH HOH . H 7 HOH A 30 630 627 HOH HOH . H 7 HOH A 31 631 644 HOH HOH . H 7 HOH A 32 632 643 HOH HOH . H 7 HOH A 33 633 625 HOH HOH . H 7 HOH A 34 634 638 HOH HOH . H 7 HOH A 35 635 641 HOH HOH . H 7 HOH A 36 636 640 HOH HOH . H 7 HOH A 37 637 629 HOH HOH . H 7 HOH A 38 638 634 HOH HOH . H 7 HOH A 39 639 646 HOH HOH . H 7 HOH A 40 640 649 HOH HOH . H 7 HOH A 41 641 633 HOH HOH . H 7 HOH A 42 642 637 HOH HOH . H 7 HOH A 43 643 639 HOH HOH . H 7 HOH A 44 644 636 HOH HOH . H 7 HOH A 45 645 650 HOH HOH . H 7 HOH A 46 646 648 HOH HOH . H 7 HOH A 47 647 656 HOH HOH . H 7 HOH A 48 648 645 HOH HOH . H 7 HOH A 49 649 642 HOH HOH . H 7 HOH A 50 650 647 HOH HOH . H 7 HOH A 51 651 635 HOH HOH . H 7 HOH A 52 652 653 HOH HOH . H 7 HOH A 53 653 657 HOH HOH . H 7 HOH A 54 654 651 HOH HOH . H 7 HOH A 55 655 659 HOH HOH . H 7 HOH A 56 656 660 HOH HOH . H 7 HOH A 57 657 665 HOH HOH . H 7 HOH A 58 658 655 HOH HOH . H 7 HOH A 59 659 658 HOH HOH . H 7 HOH A 60 660 662 HOH HOH . H 7 HOH A 61 661 652 HOH HOH . H 7 HOH A 62 662 661 HOH HOH . H 7 HOH A 63 663 654 HOH HOH . H 7 HOH A 64 664 666 HOH HOH . H 7 HOH A 65 665 672 HOH HOH . H 7 HOH A 66 666 667 HOH HOH . H 7 HOH A 67 667 669 HOH HOH . H 7 HOH A 68 668 668 HOH HOH . H 7 HOH A 69 669 664 HOH HOH . H 7 HOH A 70 670 663 HOH HOH . H 7 HOH A 71 671 670 HOH HOH . H 7 HOH A 72 672 671 HOH HOH . H 7 HOH A 73 673 675 HOH HOH . H 7 HOH A 74 674 678 HOH HOH . H 7 HOH A 75 675 673 HOH HOH . H 7 HOH A 76 676 679 HOH HOH . H 7 HOH A 77 677 676 HOH HOH . H 7 HOH A 78 678 685 HOH HOH . H 7 HOH A 79 679 686 HOH HOH . H 7 HOH A 80 680 680 HOH HOH . H 7 HOH A 81 681 674 HOH HOH . H 7 HOH A 82 682 681 HOH HOH . H 7 HOH A 83 683 677 HOH HOH . H 7 HOH A 84 684 694 HOH HOH . H 7 HOH A 85 685 693 HOH HOH . H 7 HOH A 86 686 682 HOH HOH . H 7 HOH A 87 687 683 HOH HOH . H 7 HOH A 88 688 697 HOH HOH . H 7 HOH A 89 689 690 HOH HOH . H 7 HOH A 90 690 689 HOH HOH . H 7 HOH A 91 691 692 HOH HOH . H 7 HOH A 92 692 688 HOH HOH . H 7 HOH A 93 693 702 HOH HOH . H 7 HOH A 94 694 687 HOH HOH . H 7 HOH A 95 695 695 HOH HOH . H 7 HOH A 96 696 684 HOH HOH . H 7 HOH A 97 697 691 HOH HOH . H 7 HOH A 98 698 696 HOH HOH . H 7 HOH A 99 699 700 HOH HOH . H 7 HOH A 100 700 699 HOH HOH . H 7 HOH A 101 701 706 HOH HOH . H 7 HOH A 102 702 704 HOH HOH . H 7 HOH A 103 703 698 HOH HOH . H 7 HOH A 104 704 701 HOH HOH . H 7 HOH A 105 705 714 HOH HOH . H 7 HOH A 106 706 705 HOH HOH . H 7 HOH A 107 707 707 HOH HOH . H 7 HOH A 108 708 709 HOH HOH . H 7 HOH A 109 709 708 HOH HOH . H 7 HOH A 110 710 717 HOH HOH . H 7 HOH A 111 711 723 HOH HOH . H 7 HOH A 112 712 711 HOH HOH . H 7 HOH A 113 713 719 HOH HOH . H 7 HOH A 114 714 715 HOH HOH . H 7 HOH A 115 715 703 HOH HOH . H 7 HOH A 116 716 710 HOH HOH . H 7 HOH A 117 717 713 HOH HOH . H 7 HOH A 118 718 716 HOH HOH . H 7 HOH A 119 719 720 HOH HOH . H 7 HOH A 120 720 722 HOH HOH . H 7 HOH A 121 721 712 HOH HOH . H 7 HOH A 122 722 728 HOH HOH . H 7 HOH A 123 723 721 HOH HOH . H 7 HOH A 124 724 732 HOH HOH . H 7 HOH A 125 725 731 HOH HOH . H 7 HOH A 126 726 727 HOH HOH . H 7 HOH A 127 727 725 HOH HOH . H 7 HOH A 128 728 726 HOH HOH . H 7 HOH A 129 729 729 HOH HOH . H 7 HOH A 130 730 724 HOH HOH . H 7 HOH A 131 731 735 HOH HOH . H 7 HOH A 132 732 730 HOH HOH . H 7 HOH A 133 733 734 HOH HOH . H 7 HOH A 134 734 736 HOH HOH . H 7 HOH A 135 735 718 HOH HOH . H 7 HOH A 136 736 738 HOH HOH . H 7 HOH A 137 737 745 HOH HOH . H 7 HOH A 138 738 733 HOH HOH . H 7 HOH A 139 739 746 HOH HOH . H 7 HOH A 140 740 737 HOH HOH . H 7 HOH A 141 741 741 HOH HOH . H 7 HOH A 142 742 744 HOH HOH . H 7 HOH A 143 743 739 HOH HOH . H 7 HOH A 144 744 742 HOH HOH . H 7 HOH A 145 745 743 HOH HOH . H 7 HOH A 146 746 747 HOH HOH . H 7 HOH A 147 747 750 HOH HOH . H 7 HOH A 148 748 740 HOH HOH . H 7 HOH A 149 749 749 HOH HOH . H 7 HOH A 150 750 748 HOH HOH . H 7 HOH A 151 751 751 HOH HOH . H 7 HOH A 152 752 755 HOH HOH . H 7 HOH A 153 753 753 HOH HOH . H 7 HOH A 154 754 752 HOH HOH . H 7 HOH A 155 755 756 HOH HOH . H 7 HOH A 156 756 754 HOH HOH . H 7 HOH A 157 757 770 HOH HOH . H 7 HOH A 158 758 762 HOH HOH . H 7 HOH A 159 759 758 HOH HOH . H 7 HOH A 160 760 757 HOH HOH . H 7 HOH A 161 761 768 HOH HOH . H 7 HOH A 162 762 759 HOH HOH . H 7 HOH A 163 763 760 HOH HOH . H 7 HOH A 164 764 775 HOH HOH . H 7 HOH A 165 765 765 HOH HOH . H 7 HOH A 166 766 774 HOH HOH . H 7 HOH A 167 767 767 HOH HOH . H 7 HOH A 168 768 764 HOH HOH . H 7 HOH A 169 769 766 HOH HOH . H 7 HOH A 170 770 769 HOH HOH . H 7 HOH A 171 771 771 HOH HOH . H 7 HOH A 172 772 761 HOH HOH . H 7 HOH A 173 773 777 HOH HOH . H 7 HOH A 174 774 772 HOH HOH . H 7 HOH A 175 775 763 HOH HOH . H 7 HOH A 176 776 773 HOH HOH . H 7 HOH A 177 777 779 HOH HOH . H 7 HOH A 178 778 776 HOH HOH . H 7 HOH A 179 779 778 HOH HOH . H 7 HOH A 180 780 781 HOH HOH . H 7 HOH A 181 781 780 HOH HOH . H 7 HOH A 182 782 784 HOH HOH . H 7 HOH A 183 783 783 HOH HOH . H 7 HOH A 184 784 788 HOH HOH . H 7 HOH A 185 785 787 HOH HOH . H 7 HOH A 186 786 790 HOH HOH . H 7 HOH A 187 787 786 HOH HOH . H 7 HOH A 188 788 782 HOH HOH . H 7 HOH A 189 789 785 HOH HOH . H 7 HOH A 190 790 794 HOH HOH . H 7 HOH A 191 791 795 HOH HOH . H 7 HOH A 192 792 791 HOH HOH . H 7 HOH A 193 793 793 HOH HOH . H 7 HOH A 194 794 789 HOH HOH . H 7 HOH A 195 795 792 HOH HOH . H 7 HOH A 196 796 802 HOH HOH . H 7 HOH A 197 797 797 HOH HOH . H 7 HOH A 198 798 796 HOH HOH . H 7 HOH A 199 799 799 HOH HOH . H 7 HOH A 200 800 803 HOH HOH . H 7 HOH A 201 801 805 HOH HOH . H 7 HOH A 202 802 798 HOH HOH . H 7 HOH A 203 803 801 HOH HOH . H 7 HOH A 204 804 804 HOH HOH . H 7 HOH A 205 805 800 HOH HOH . H 7 HOH A 206 806 808 HOH HOH . H 7 HOH A 207 807 809 HOH HOH . H 7 HOH A 208 808 806 HOH HOH . H 7 HOH A 209 809 807 HOH HOH . H 7 HOH A 210 810 811 HOH HOH . H 7 HOH A 211 811 810 HOH HOH . H 7 HOH A 212 812 812 HOH HOH . H 7 HOH A 213 813 814 HOH HOH . H 7 HOH A 214 814 815 HOH HOH . H 7 HOH A 215 815 813 HOH HOH . H 7 HOH A 216 816 816 HOH HOH . H 7 HOH A 217 817 817 HOH HOH . H 7 HOH A 218 818 818 HOH HOH . H 7 HOH A 219 819 819 HOH HOH . H 7 HOH A 220 820 820 HOH HOH . H 7 HOH A 221 821 822 HOH HOH . H 7 HOH A 222 822 823 HOH HOH . H 7 HOH A 223 823 821 HOH HOH . H 7 HOH A 224 824 824 HOH HOH . H 7 HOH A 225 825 825 HOH HOH . H 7 HOH A 226 826 826 HOH HOH . H 7 HOH A 227 827 827 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 F _atom_site.label_entity_id 5 _atom_site.Cartn_x -3.66 _atom_site.Cartn_y 6.132 _atom_site.Cartn_z 35.901 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 18.93 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 506 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #