data_4GM7 # _model_server_result.job_id -_qVTk617BEgpTJwmY4hfg _model_server_result.datetime_utc '2024-11-23 07:52:20' _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 4gm7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":618}' # _entry.id 4GM7 # _exptl.entry_id 4GM7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 103.3 _cell.angle_gamma 90 _cell.entry_id 4GM7 _cell.length_a 54.05 _cell.length_b 80.23 _cell.length_c 76.04 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GM7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W _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 9 _struct_asym.id R _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 NAG _pdbx_entity_branch_link.comp_id_2 NAG _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 2 n B NAG 1 B 1 NAG A 601 NAG 2 n B NAG 2 B 2 NAG A 602 NAG # 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 6 A CYS 6 1_555 A SG CYS 167 A CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf2 A SG CYS 15 A CYS 15 1_555 A SG CYS 28 A CYS 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 129 A CYS 129 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 133 A CYS 133 1_555 A SG CYS 157 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 ? disulf ? disulf5 A SG CYS 237 A CYS 237 1_555 A SG CYS 248 A CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 456 A CYS 456 1_555 A SG CYS 513 A CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf7 A SG CYS 554 A CYS 554 1_555 A SG CYS 579 A CYS 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 95 A ASN 95 1_555 D C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A OD2 ASP 108 A ASP 108 1_555 C CMD HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.585 ? covale ? covale3 A C PRO 197 A PRO 197 1_555 A N SEP 198 A SEP 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C SEP 198 A SEP 198 1_555 A N LEU 199 A LEU 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale5 A ND2 ASN 205 A ASN 205 1_555 E C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 A ND2 ASN 241 A ASN 241 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 A OE2 GLU 258 A GLU 258 1_555 C CMB HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.58 ? covale ? covale8 A ND2 ASN 332 A ASN 332 1_555 F C1 NAG . A NAG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale9 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? metalc ? metalc1 A O ASP 110 A ASP 110 1_555 O CA CA . A CA 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc2 A OD1 ASP 110 A ASP 110 1_555 O CA CA . A CA 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc3 A O THR 184 A THR 184 1_555 O CA CA . A CA 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc4 A OG1 THR 184 A THR 184 1_555 O CA CA . A CA 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc5 A O PHE 186 A PHE 186 1_555 O CA CA . A CA 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc6 A OD1 ASP 188 A ASP 188 1_555 O CA CA . A CA 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc7 A OG SER 190 A SER 190 1_555 O CA CA . A CA 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc8 A NE2 HIS 351 A HIS 351 1_555 C FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc9 C FE HEM . A HEM 601 1_555 W O HOH . A HOH 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 138 n n C1 C2 GOL sing 139 n n C1 H11 GOL sing 140 n n C1 H12 GOL sing 141 n n O1 HO1 GOL sing 142 n n C2 O2 GOL sing 143 n n C2 C3 GOL sing 144 n n C2 H2 GOL sing 145 n n O2 HO2 GOL sing 146 n n C3 O3 GOL sing 147 n n C3 H31 GOL sing 148 n n C3 H32 GOL sing 149 n n O3 HO3 GOL sing 150 n n # _atom_sites.entry_id 4GM7 _atom_sites.fract_transf_matrix[1][1] 0.018501 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004374 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012464 _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] 0.013513 _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 3 HEM A 1 601 601 HEM HEM . D 4 NAG A 1 602 596 NAG NAG . E 4 NAG A 1 603 599 NAG NAG . F 4 NAG A 1 606 604 NAG NAG . G 5 IOD A 1 607 607 IOD IOD . H 5 IOD A 1 608 608 IOD IOD . I 5 IOD A 1 609 609 IOD IOD . J 5 IOD A 1 610 610 IOD IOD . K 5 IOD A 1 611 611 IOD IOD . L 5 IOD A 1 612 615 IOD IOD . M 5 IOD A 1 613 616 IOD IOD . N 5 IOD A 1 614 617 IOD IOD . O 6 CA A 1 615 606 CA CA . P 7 SCN A 1 616 620 SCN SCN . Q 8 PEG A 1 617 619 PEG PEG . R 9 GOL A 1 618 621 GOL GOL . S 10 EDO A 1 619 623 EDO EDO . T 10 EDO A 1 620 624 EDO EDO . U 10 EDO A 1 621 625 EDO EDO . V 11 HCI A 1 622 622 HCI HCI . W 12 HOH A 1 701 613 HOH HOH . W 12 HOH A 2 702 615 HOH HOH . W 12 HOH A 3 703 616 HOH HOH . W 12 HOH A 4 704 617 HOH HOH . W 12 HOH A 5 705 618 HOH HOH . W 12 HOH A 6 706 619 HOH HOH . W 12 HOH A 7 707 620 HOH HOH . W 12 HOH A 8 708 625 HOH HOH . W 12 HOH A 9 709 628 HOH HOH . W 12 HOH A 10 710 629 HOH HOH . W 12 HOH A 11 711 630 HOH HOH . W 12 HOH A 12 712 633 HOH HOH . W 12 HOH A 13 713 634 HOH HOH . W 12 HOH A 14 714 635 HOH HOH . W 12 HOH A 15 715 636 HOH HOH . W 12 HOH A 16 716 637 HOH HOH . W 12 HOH A 17 717 638 HOH HOH . W 12 HOH A 18 718 639 HOH HOH . W 12 HOH A 19 719 640 HOH HOH . W 12 HOH A 20 720 641 HOH HOH . W 12 HOH A 21 721 642 HOH HOH . W 12 HOH A 22 722 644 HOH HOH . W 12 HOH A 23 723 649 HOH HOH . W 12 HOH A 24 724 650 HOH HOH . W 12 HOH A 25 725 651 HOH HOH . W 12 HOH A 26 726 652 HOH HOH . W 12 HOH A 27 727 653 HOH HOH . W 12 HOH A 28 728 662 HOH HOH . W 12 HOH A 29 729 663 HOH HOH . W 12 HOH A 30 730 665 HOH HOH . W 12 HOH A 31 731 668 HOH HOH . W 12 HOH A 32 732 671 HOH HOH . W 12 HOH A 33 733 674 HOH HOH . W 12 HOH A 34 734 676 HOH HOH . W 12 HOH A 35 735 680 HOH HOH . W 12 HOH A 36 736 681 HOH HOH . W 12 HOH A 37 737 683 HOH HOH . W 12 HOH A 38 738 684 HOH HOH . W 12 HOH A 39 739 685 HOH HOH . W 12 HOH A 40 740 686 HOH HOH . W 12 HOH A 41 741 687 HOH HOH . W 12 HOH A 42 742 688 HOH HOH . W 12 HOH A 43 743 689 HOH HOH . W 12 HOH A 44 744 690 HOH HOH . W 12 HOH A 45 745 696 HOH HOH . W 12 HOH A 46 746 697 HOH HOH . W 12 HOH A 47 747 698 HOH HOH . W 12 HOH A 48 748 701 HOH HOH . W 12 HOH A 49 749 703 HOH HOH . W 12 HOH A 50 750 706 HOH HOH . W 12 HOH A 51 751 707 HOH HOH . W 12 HOH A 52 752 711 HOH HOH . W 12 HOH A 53 753 712 HOH HOH . W 12 HOH A 54 754 713 HOH HOH . W 12 HOH A 55 755 714 HOH HOH . W 12 HOH A 56 756 715 HOH HOH . W 12 HOH A 57 757 716 HOH HOH . W 12 HOH A 58 758 727 HOH HOH . W 12 HOH A 59 759 728 HOH HOH . W 12 HOH A 60 760 729 HOH HOH . W 12 HOH A 61 761 732 HOH HOH . W 12 HOH A 62 762 733 HOH HOH . W 12 HOH A 63 763 736 HOH HOH . W 12 HOH A 64 764 738 HOH HOH . W 12 HOH A 65 765 740 HOH HOH . W 12 HOH A 66 766 741 HOH HOH . W 12 HOH A 67 767 745 HOH HOH . W 12 HOH A 68 768 746 HOH HOH . W 12 HOH A 69 769 757 HOH HOH . W 12 HOH A 70 770 760 HOH HOH . W 12 HOH A 71 771 762 HOH HOH . W 12 HOH A 72 772 763 HOH HOH . W 12 HOH A 73 773 768 HOH HOH . W 12 HOH A 74 774 1 HOH HOH . W 12 HOH A 75 775 2 HOH HOH . W 12 HOH A 76 776 4 HOH HOH . W 12 HOH A 77 777 7 HOH HOH . W 12 HOH A 78 778 8 HOH HOH . W 12 HOH A 79 779 9 HOH HOH . W 12 HOH A 80 780 10 HOH HOH . W 12 HOH A 81 781 11 HOH HOH . W 12 HOH A 82 782 12 HOH HOH . W 12 HOH A 83 783 13 HOH HOH . W 12 HOH A 84 784 15 HOH HOH . W 12 HOH A 85 785 18 HOH HOH . W 12 HOH A 86 786 19 HOH HOH . W 12 HOH A 87 787 21 HOH HOH . W 12 HOH A 88 788 22 HOH HOH . W 12 HOH A 89 789 23 HOH HOH . W 12 HOH A 90 790 24 HOH HOH . W 12 HOH A 91 791 25 HOH HOH . W 12 HOH A 92 792 26 HOH HOH . W 12 HOH A 93 793 27 HOH HOH . W 12 HOH A 94 794 28 HOH HOH . W 12 HOH A 95 795 29 HOH HOH . W 12 HOH A 96 796 33 HOH HOH . W 12 HOH A 97 797 34 HOH HOH . W 12 HOH A 98 798 35 HOH HOH . W 12 HOH A 99 799 36 HOH HOH . W 12 HOH A 100 800 37 HOH HOH . W 12 HOH A 101 801 38 HOH HOH . W 12 HOH A 102 802 39 HOH HOH . W 12 HOH A 103 803 40 HOH HOH . W 12 HOH A 104 804 41 HOH HOH . W 12 HOH A 105 805 42 HOH HOH . W 12 HOH A 106 806 44 HOH HOH . W 12 HOH A 107 807 46 HOH HOH . W 12 HOH A 108 808 47 HOH HOH . W 12 HOH A 109 809 49 HOH HOH . W 12 HOH A 110 810 50 HOH HOH . W 12 HOH A 111 811 51 HOH HOH . W 12 HOH A 112 812 52 HOH HOH . W 12 HOH A 113 813 54 HOH HOH . W 12 HOH A 114 814 55 HOH HOH . W 12 HOH A 115 815 60 HOH HOH . W 12 HOH A 116 816 64 HOH HOH . W 12 HOH A 117 817 65 HOH HOH . W 12 HOH A 118 818 66 HOH HOH . W 12 HOH A 119 819 67 HOH HOH . W 12 HOH A 120 820 68 HOH HOH . W 12 HOH A 121 821 69 HOH HOH . W 12 HOH A 122 822 70 HOH HOH . W 12 HOH A 123 823 71 HOH HOH . W 12 HOH A 124 824 72 HOH HOH . W 12 HOH A 125 825 73 HOH HOH . W 12 HOH A 126 826 74 HOH HOH . W 12 HOH A 127 827 75 HOH HOH . W 12 HOH A 128 828 76 HOH HOH . W 12 HOH A 129 829 79 HOH HOH . W 12 HOH A 130 830 80 HOH HOH . W 12 HOH A 131 831 81 HOH HOH . W 12 HOH A 132 832 82 HOH HOH . W 12 HOH A 133 833 83 HOH HOH . W 12 HOH A 134 834 85 HOH HOH . W 12 HOH A 135 835 88 HOH HOH . W 12 HOH A 136 836 89 HOH HOH . W 12 HOH A 137 837 91 HOH HOH . W 12 HOH A 138 838 92 HOH HOH . W 12 HOH A 139 839 94 HOH HOH . W 12 HOH A 140 840 96 HOH HOH . W 12 HOH A 141 841 97 HOH HOH . W 12 HOH A 142 842 98 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 C1 GOL . . . R 9 -1.239 3.389 9.066 1 50.33 ? C1 GOL 618 A 1 HETATM 2 O O1 GOL . . . R 9 -0.802 4.125 10.169 1 51.69 ? O1 GOL 618 A 1 HETATM 3 C C2 GOL . . . R 9 -2.061 2.154 9.436 1 48.95 ? C2 GOL 618 A 1 HETATM 4 O O2 GOL . . . R 9 -1.312 1.288 10.217 1 47.61 ? O2 GOL 618 A 1 HETATM 5 C C3 GOL . . . R 9 -2.584 1.464 8.198 1 49 ? C3 GOL 618 A 1 HETATM 6 O O3 GOL . . . R 9 -2.863 0.082 8.482 1 51.41 ? O3 GOL 618 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #