data_2BDM # _model_server_result.job_id NLB1yuLm4yvJf_1nzhGclw _model_server_result.datetime_utc '2024-10-18 04:35:02' _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 2bdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":505}' # _entry.id 2BDM # _exptl.entry_id 2BDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 494.573 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE _entity.pdbx_number_of_molecules 4 _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 2BDM _cell.length_a 203.21 _cell.length_b 203.21 _cell.length_c 103.45 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 1,2 A,B,C,D,E,F,G,H,I,J 3 1,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 203.21 0 51.725 3 'crystal symmetry operation' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 17.241667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I 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 metalc ? metalc1 A SG CYS 417 A CYS 436 1_555 B FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc2 B FE HEM . A HEM 500 1_555 C NAD TMI . A TMI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? # _chem_comp.formula 'C23 H42 O11' _chem_comp.formula_weight 494.573 _chem_comp.id CM5 _chem_comp.mon_nstd_flag . _chem_comp.name 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE;CYMAL-5' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C7 C8 CM5 sing 70 n n C7 C6 CM5 sing 71 n n C7 H71 CM5 sing 72 n n C7 H72 CM5 sing 73 n n C8 C9 CM5 sing 74 n n C8 H81 CM5 sing 75 n n C8 H82 CM5 sing 76 n n C9 C10 CM5 sing 77 n n C9 H91 CM5 sing 78 n n C9 H92 CM5 sing 79 n n C10 C11 CM5 sing 80 n n C10 H101 CM5 sing 81 n n C10 H102 CM5 sing 82 n n C11 C6 CM5 sing 83 n n C11 H111 CM5 sing 84 n n C11 H112 CM5 sing 85 n n C6 C5 CM5 sing 86 n n C6 H6 CM5 sing 87 n n C5 C4 CM5 sing 88 n n C5 H51 CM5 sing 89 n n C5 H52 CM5 sing 90 n n C4 C3 CM5 sing 91 n n C4 H41 CM5 sing 92 n n C4 H42 CM5 sing 93 n n C3 C2 CM5 sing 94 n n C3 H31A CM5 sing 95 n n C3 H32A CM5 sing 96 n n C2 C1 CM5 sing 97 n n C2 H21A CM5 sing 98 n n C2 H22A CM5 sing 99 n n C1 O12 CM5 sing 100 n n C1 H11 CM5 sing 101 n n C1 H12 CM5 sing 102 n n O12 C13 CM5 sing 103 n n C13 C18 CM5 sing 104 n n C13 O14 CM5 sing 105 n n C13 H13 CM5 sing 106 n n C18 O22 CM5 sing 107 n n C18 C17 CM5 sing 108 n n C18 H18 CM5 sing 109 n n O22 H22 CM5 sing 110 n n C17 O21 CM5 sing 111 n n C17 C16 CM5 sing 112 n n C17 H17 CM5 sing 113 n n O21 H21 CM5 sing 114 n n O14 C15 CM5 sing 115 n n C15 C19 CM5 sing 116 n n C15 C16 CM5 sing 117 n n C15 H15 CM5 sing 118 n n C19 O20 CM5 sing 119 n n C19 H191 CM5 sing 120 n n C19 H192 CM5 sing 121 n n O20 H20 CM5 sing 122 n n C16 O23 CM5 sing 123 n n C16 H16 CM5 sing 124 n n O23 C24 CM5 sing 125 n n C24 O25 CM5 sing 126 n n C24 C29 CM5 sing 127 n n C24 H24 CM5 sing 128 n n O25 C26 CM5 sing 129 n n C26 C30 CM5 sing 130 n n C26 C27 CM5 sing 131 n n C26 H26 CM5 sing 132 n n C30 O31 CM5 sing 133 n n C30 H301 CM5 sing 134 n n C30 H302 CM5 sing 135 n n O31 H31 CM5 sing 136 n n C27 O32 CM5 sing 137 n n C27 C28 CM5 sing 138 n n C27 H27 CM5 sing 139 n n O32 H32 CM5 sing 140 n n C28 O33 CM5 sing 141 n n C28 C29 CM5 sing 142 n n C28 H28 CM5 sing 143 n n O33 H33 CM5 sing 144 n n C29 O34 CM5 sing 145 n n C29 H29 CM5 sing 146 n n O34 H34 CM5 sing 147 n n # _atom_sites.entry_id 2BDM _atom_sites.fract_transf_matrix[1][1] 0.004921 _atom_sites.fract_transf_matrix[1][2] 0.002841 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005682 _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] 0.009667 _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 B 2 HEM A 1 500 500 HEM HEM . C 3 TMI A 1 501 501 TMI TMI . D 3 TMI A 1 502 502 TMI TMI . E 3 TMI A 1 503 503 TMI TMI . F 4 CM5 A 1 504 504 CM5 CM5 . G 4 CM5 A 1 505 505 CM5 CM5 . H 4 CM5 A 1 506 506 CM5 CM5 . I 4 CM5 A 1 507 507 CM5 CM5 . J 5 HOH A 1 601 601 HOH HOH . J 5 HOH A 2 602 602 HOH HOH . J 5 HOH A 3 603 603 HOH HOH . J 5 HOH A 4 604 604 HOH HOH . J 5 HOH A 5 605 605 HOH HOH . J 5 HOH A 6 606 606 HOH HOH . J 5 HOH A 7 607 607 HOH HOH . J 5 HOH A 8 608 608 HOH HOH . J 5 HOH A 9 609 609 HOH HOH . J 5 HOH A 10 610 610 HOH HOH . J 5 HOH A 11 611 611 HOH HOH . J 5 HOH A 12 612 612 HOH HOH . J 5 HOH A 13 613 613 HOH HOH . J 5 HOH A 14 614 614 HOH HOH . J 5 HOH A 15 615 615 HOH HOH . J 5 HOH A 16 616 616 HOH HOH . J 5 HOH A 17 617 617 HOH HOH . J 5 HOH A 18 618 618 HOH HOH . J 5 HOH A 19 619 619 HOH HOH . J 5 HOH A 20 620 620 HOH HOH . J 5 HOH A 21 621 621 HOH HOH . J 5 HOH A 22 622 622 HOH HOH . J 5 HOH A 23 623 623 HOH HOH . J 5 HOH A 24 624 624 HOH HOH . J 5 HOH A 25 625 625 HOH HOH . J 5 HOH A 26 626 626 HOH HOH . J 5 HOH A 27 627 627 HOH HOH . J 5 HOH A 28 628 628 HOH HOH . J 5 HOH A 29 629 629 HOH HOH . J 5 HOH A 30 630 630 HOH HOH . J 5 HOH A 31 631 631 HOH HOH . J 5 HOH A 32 632 632 HOH HOH . J 5 HOH A 33 633 633 HOH HOH . J 5 HOH A 34 634 634 HOH HOH . J 5 HOH A 35 635 635 HOH HOH . J 5 HOH A 36 636 636 HOH HOH . J 5 HOH A 37 637 637 HOH HOH . J 5 HOH A 38 638 638 HOH HOH . J 5 HOH A 39 639 639 HOH HOH . J 5 HOH A 40 640 640 HOH HOH . J 5 HOH A 41 641 641 HOH HOH . J 5 HOH A 42 642 642 HOH HOH . J 5 HOH A 43 643 643 HOH HOH . J 5 HOH A 44 644 644 HOH HOH . J 5 HOH A 45 645 645 HOH HOH . J 5 HOH A 46 646 646 HOH HOH . J 5 HOH A 47 647 647 HOH HOH . J 5 HOH A 48 648 648 HOH HOH . J 5 HOH A 49 649 649 HOH HOH . J 5 HOH A 50 650 650 HOH HOH . J 5 HOH A 51 651 651 HOH HOH . J 5 HOH A 52 652 652 HOH HOH . J 5 HOH A 53 653 653 HOH HOH . J 5 HOH A 54 654 654 HOH HOH . J 5 HOH A 55 655 655 HOH HOH . J 5 HOH A 56 656 656 HOH HOH . J 5 HOH A 57 657 657 HOH HOH . J 5 HOH A 58 658 658 HOH HOH . J 5 HOH A 59 659 659 HOH HOH . J 5 HOH A 60 660 660 HOH HOH . J 5 HOH A 61 661 661 HOH HOH . J 5 HOH A 62 662 662 HOH HOH . J 5 HOH A 63 663 663 HOH HOH . J 5 HOH A 64 664 664 HOH HOH . J 5 HOH A 65 665 665 HOH HOH . J 5 HOH A 66 666 666 HOH HOH . J 5 HOH A 67 667 667 HOH HOH . J 5 HOH A 68 668 668 HOH HOH . J 5 HOH A 69 669 669 HOH HOH . J 5 HOH A 70 670 670 HOH HOH . J 5 HOH A 71 671 671 HOH HOH . J 5 HOH A 72 672 672 HOH HOH . J 5 HOH A 73 673 673 HOH HOH . J 5 HOH A 74 674 674 HOH HOH . J 5 HOH A 75 675 675 HOH HOH . J 5 HOH A 76 676 676 HOH HOH . J 5 HOH A 77 677 677 HOH HOH . J 5 HOH A 78 678 678 HOH HOH . J 5 HOH A 79 679 679 HOH HOH . J 5 HOH A 80 680 680 HOH HOH . J 5 HOH A 81 681 681 HOH HOH . J 5 HOH A 82 682 682 HOH HOH . J 5 HOH A 83 683 683 HOH HOH . J 5 HOH A 84 684 684 HOH HOH . J 5 HOH A 85 685 685 HOH HOH . J 5 HOH A 86 686 686 HOH HOH . J 5 HOH A 87 687 687 HOH HOH . J 5 HOH A 88 688 688 HOH HOH . J 5 HOH A 89 689 689 HOH HOH . J 5 HOH A 90 690 690 HOH HOH . J 5 HOH A 91 691 691 HOH HOH . J 5 HOH A 92 692 692 HOH HOH . J 5 HOH A 93 693 693 HOH HOH . J 5 HOH A 94 694 694 HOH HOH . J 5 HOH A 95 695 695 HOH HOH . J 5 HOH A 96 696 696 HOH HOH . J 5 HOH A 97 697 697 HOH HOH . J 5 HOH A 98 698 698 HOH HOH . J 5 HOH A 99 699 699 HOH HOH . J 5 HOH A 100 700 700 HOH HOH . J 5 HOH A 101 701 701 HOH HOH . J 5 HOH A 102 702 702 HOH HOH . J 5 HOH A 103 703 703 HOH HOH . J 5 HOH A 104 704 704 HOH HOH . J 5 HOH A 105 705 705 HOH HOH . J 5 HOH A 106 706 706 HOH HOH . J 5 HOH A 107 707 707 HOH HOH . J 5 HOH A 108 708 708 HOH HOH . J 5 HOH A 109 709 709 HOH HOH . J 5 HOH A 110 710 710 HOH HOH . J 5 HOH A 111 711 711 HOH HOH . J 5 HOH A 112 712 712 HOH HOH . J 5 HOH A 113 713 713 HOH HOH . J 5 HOH A 114 714 714 HOH HOH . J 5 HOH A 115 715 715 HOH HOH . J 5 HOH A 116 716 716 HOH HOH . J 5 HOH A 117 717 717 HOH HOH . J 5 HOH A 118 718 718 HOH HOH . J 5 HOH A 119 719 719 HOH HOH . J 5 HOH A 120 720 720 HOH HOH . J 5 HOH A 121 721 721 HOH HOH . J 5 HOH A 122 722 722 HOH HOH . J 5 HOH A 123 723 723 HOH HOH . J 5 HOH A 124 724 724 HOH HOH . J 5 HOH A 125 725 725 HOH HOH . J 5 HOH A 126 726 726 HOH HOH . J 5 HOH A 127 727 727 HOH HOH . J 5 HOH A 128 728 728 HOH HOH . J 5 HOH A 129 729 729 HOH HOH . J 5 HOH A 130 730 730 HOH HOH . J 5 HOH A 131 731 731 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C7 CM5 . . . G 4 100.166 35.84 22.524 1 60.16 ? C7 CM5 505 A 1 HETATM 2 C C8 CM5 . . . G 4 101.069 34.938 23.37 1 64.53 ? C8 CM5 505 A 1 HETATM 3 C C9 CM5 . . . G 4 101.704 33.851 22.498 1 62.53 ? C9 CM5 505 A 1 HETATM 4 C C10 CM5 . . . G 4 102.49 34.48 21.345 1 60.68 ? C10 CM5 505 A 1 HETATM 5 C C11 CM5 . . . G 4 101.585 35.393 20.513 1 64.4 ? C11 CM5 505 A 1 HETATM 6 C C6 CM5 . . . G 4 100.948 36.487 21.377 1 60.87 ? C6 CM5 505 A 1 HETATM 7 C C5 CM5 . . . G 4 100.014 37.322 20.499 1 65.77 ? C5 CM5 505 A 1 HETATM 8 C C4 CM5 . . . G 4 99.279 38.41 21.284 1 65.47 ? C4 CM5 505 A 1 HETATM 9 C C3 CM5 . . . G 4 98.226 39.089 20.404 1 79.68 ? C3 CM5 505 A 1 HETATM 10 C C2 CM5 . . . G 4 98.83 40.109 19.438 1 91.11 ? C2 CM5 505 A 1 HETATM 11 C C1 CM5 . . . G 4 99.225 41.383 20.188 1 96.14 ? C1 CM5 505 A 1 HETATM 12 O O12 CM5 . . . G 4 98.048 41.885 20.838 1 90.03 ? O12 CM5 505 A 1 HETATM 13 C C13 CM5 . . . G 4 97.619 43.119 20.244 1 83.85 ? C13 CM5 505 A 1 HETATM 14 C C18 CM5 . . . G 4 96.186 43.408 20.697 1 74.03 ? C18 CM5 505 A 1 HETATM 15 O O22 CM5 . . . G 4 95.314 42.38 20.221 1 76.79 ? O22 CM5 505 A 1 HETATM 16 C C17 CM5 . . . G 4 95.742 44.761 20.141 1 78.81 ? C17 CM5 505 A 1 HETATM 17 O O21 CM5 . . . G 4 94.442 45.072 20.649 1 86.32 ? O21 CM5 505 A 1 HETATM 18 O O14 CM5 . . . G 4 98.492 44.184 20.659 1 81.23 ? O14 CM5 505 A 1 HETATM 19 C C15 CM5 . . . G 4 98.13 45.471 20.127 1 75.76 ? C15 CM5 505 A 1 HETATM 20 C C19 CM5 . . . G 4 99.109 46.481 20.731 1 79.86 ? C19 CM5 505 A 1 HETATM 21 O O20 CM5 . . . G 4 100.454 46.032 20.542 1 65.24 ? O20 CM5 505 A 1 HETATM 22 C C16 CM5 . . . G 4 96.722 45.859 20.561 1 74.52 ? C16 CM5 505 A 1 HETATM 23 O O23 CM5 . . . G 4 96.295 47.085 19.949 1 97.48 ? O23 CM5 505 A 1 HETATM 24 C C24 CM5 . . . G 4 96.524 48.217 20.802 1 122.76 ? C24 CM5 505 A 1 HETATM 25 O O25 CM5 . . . G 4 97.704 48.915 20.366 1 139.93 ? O25 CM5 505 A 1 HETATM 26 C C26 CM5 . . . G 4 97.636 49.311 18.985 1 125.71 ? C26 CM5 505 A 1 HETATM 27 C C30 CM5 . . . G 4 98.957 49.982 18.603 1 106.12 ? C30 CM5 505 A 1 HETATM 28 O O31 CM5 . . . G 4 98.929 50.355 17.223 1 104.75 ? O31 CM5 505 A 1 HETATM 29 C C27 CM5 . . . G 4 96.472 50.286 18.774 1 133.64 ? C27 CM5 505 A 1 HETATM 30 O O32 CM5 . . . G 4 96.347 50.577 17.38 1 113.11 ? O32 CM5 505 A 1 HETATM 31 C C28 CM5 . . . G 4 95.165 49.661 19.269 1 136.09 ? C28 CM5 505 A 1 HETATM 32 O O33 CM5 . . . G 4 94.117 50.632 19.209 1 131.14 ? O33 CM5 505 A 1 HETATM 33 C C29 CM5 . . . G 4 95.325 49.165 20.708 1 131.35 ? C29 CM5 505 A 1 HETATM 34 O O34 CM5 . . . G 4 94.134 48.495 21.13 1 110.38 ? O34 CM5 505 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #