data_5LRM
#
_model_server_result.job_id            -BeJxjfwhGhdeT0dx_y4CQ 
_model_server_result.datetime_utc      '2025-03-03 17:02:01' 
_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          5lrm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":603}' 
#
_entry.id    5LRM 
#
_exptl.entry_id    5LRM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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 
_cell.angle_gamma         90 
_cell.entry_id            5LRM 
_cell.length_a            49.044 
_cell.length_b            49.044 
_cell.length_c            244.253 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LRM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 E 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 65 A CYS 281 1_555 A SG CYS 75 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
disulf ? disulf2 A SG CYS 140 A CYS 356 1_555 A SG CYS 148 A CYS 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc1 A OE1 GLU 30 A GLU 246 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? 
metalc ? metalc2 A OE2 GLU 30 A GLU 246 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc3 A OG1 THR 69 A THR 285 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc4 A OE1 GLU 84 A GLU 300 1_555 C ZN ZN . A ZN 602 5_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc5 A OE2 GLU 84 A GLU 300 1_555 C ZN ZN . A ZN 602 5_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc6 A NE2 HIS 179 A HIS 395 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? 
metalc ? metalc7 A OD1 ASP 249 A ASP 465 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
metalc ? metalc8 A NE2 HIS 250 A HIS 466 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc9 A NE2 HIS 262 A HIS 478 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc10 C ZN ZN . A ZN 602 1_555 F O HOH . A HOH 701 5_455 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
#
_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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     5LRM 
_atom_sites.fract_transf_matrix[1][1]    0.02039 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.02039 
_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]    0.004094 
_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 ZN A 1 601 1 ZN ZN . 
C 2 ZN A 1 602 2 ZN ZN . 
D 3 GOL A 1 603 1 GOL GOL . 
E 3 GOL A 1 604 2 GOL GOL . 
F 4 HOH A 1 701 125 HOH HOH . 
F 4 HOH A 2 702 133 HOH HOH . 
F 4 HOH A 3 703 79 HOH HOH . 
F 4 HOH A 4 704 84 HOH HOH . 
F 4 HOH A 5 705 120 HOH HOH . 
F 4 HOH A 6 706 100 HOH HOH . 
F 4 HOH A 7 707 10 HOH HOH . 
F 4 HOH A 8 708 124 HOH HOH . 
F 4 HOH A 9 709 152 HOH HOH . 
F 4 HOH A 10 710 53 HOH HOH . 
F 4 HOH A 11 711 135 HOH HOH . 
F 4 HOH A 12 712 42 HOH HOH . 
F 4 HOH A 13 713 6 HOH HOH . 
F 4 HOH A 14 714 66 HOH HOH . 
F 4 HOH A 15 715 160 HOH HOH . 
F 4 HOH A 16 716 109 HOH HOH . 
F 4 HOH A 17 717 141 HOH HOH . 
F 4 HOH A 18 718 154 HOH HOH . 
F 4 HOH A 19 719 62 HOH HOH . 
F 4 HOH A 20 720 151 HOH HOH . 
F 4 HOH A 21 721 131 HOH HOH . 
F 4 HOH A 22 722 93 HOH HOH . 
F 4 HOH A 23 723 164 HOH HOH . 
F 4 HOH A 24 724 106 HOH HOH . 
F 4 HOH A 25 725 56 HOH HOH . 
F 4 HOH A 26 726 89 HOH HOH . 
F 4 HOH A 27 727 166 HOH HOH . 
F 4 HOH A 28 728 97 HOH HOH . 
F 4 HOH A 29 729 68 HOH HOH . 
F 4 HOH A 30 730 59 HOH HOH . 
F 4 HOH A 31 731 13 HOH HOH . 
F 4 HOH A 32 732 18 HOH HOH . 
F 4 HOH A 33 733 83 HOH HOH . 
F 4 HOH A 34 734 70 HOH HOH . 
F 4 HOH A 35 735 23 HOH HOH . 
F 4 HOH A 36 736 26 HOH HOH . 
F 4 HOH A 37 737 57 HOH HOH . 
F 4 HOH A 38 738 32 HOH HOH . 
F 4 HOH A 39 739 95 HOH HOH . 
F 4 HOH A 40 740 108 HOH HOH . 
F 4 HOH A 41 741 25 HOH HOH . 
F 4 HOH A 42 742 37 HOH HOH . 
F 4 HOH A 43 743 15 HOH HOH . 
F 4 HOH A 44 744 102 HOH HOH . 
F 4 HOH A 45 745 58 HOH HOH . 
F 4 HOH A 46 746 55 HOH HOH . 
F 4 HOH A 47 747 24 HOH HOH . 
F 4 HOH A 48 748 88 HOH HOH . 
F 4 HOH A 49 749 52 HOH HOH . 
F 4 HOH A 50 750 31 HOH HOH . 
F 4 HOH A 51 751 103 HOH HOH . 
F 4 HOH A 52 752 123 HOH HOH . 
F 4 HOH A 53 753 61 HOH HOH . 
F 4 HOH A 54 754 142 HOH HOH . 
F 4 HOH A 55 755 81 HOH HOH . 
F 4 HOH A 56 756 60 HOH HOH . 
F 4 HOH A 57 757 63 HOH HOH . 
F 4 HOH A 58 758 117 HOH HOH . 
F 4 HOH A 59 759 22 HOH HOH . 
F 4 HOH A 60 760 19 HOH HOH . 
F 4 HOH A 61 761 35 HOH HOH . 
F 4 HOH A 62 762 73 HOH HOH . 
F 4 HOH A 63 763 118 HOH HOH . 
F 4 HOH A 64 764 33 HOH HOH . 
F 4 HOH A 65 765 1 HOH HOH . 
F 4 HOH A 66 766 139 HOH HOH . 
F 4 HOH A 67 767 136 HOH HOH . 
F 4 HOH A 68 768 75 HOH HOH . 
F 4 HOH A 69 769 92 HOH HOH . 
F 4 HOH A 70 770 111 HOH HOH . 
F 4 HOH A 71 771 104 HOH HOH . 
F 4 HOH A 72 772 65 HOH HOH . 
F 4 HOH A 73 773 116 HOH HOH . 
F 4 HOH A 74 774 76 HOH HOH . 
F 4 HOH A 75 775 9 HOH HOH . 
F 4 HOH A 76 776 48 HOH HOH . 
F 4 HOH A 77 777 39 HOH HOH . 
F 4 HOH A 78 778 64 HOH HOH . 
F 4 HOH A 79 779 147 HOH HOH . 
F 4 HOH A 80 780 28 HOH HOH . 
F 4 HOH A 81 781 96 HOH HOH . 
F 4 HOH A 82 782 14 HOH HOH . 
F 4 HOH A 83 783 7 HOH HOH . 
F 4 HOH A 84 784 2 HOH HOH . 
F 4 HOH A 85 785 113 HOH HOH . 
F 4 HOH A 86 786 49 HOH HOH . 
F 4 HOH A 87 787 71 HOH HOH . 
F 4 HOH A 88 788 8 HOH HOH . 
F 4 HOH A 89 789 34 HOH HOH . 
F 4 HOH A 90 790 148 HOH HOH . 
F 4 HOH A 91 791 107 HOH HOH . 
F 4 HOH A 92 792 87 HOH HOH . 
F 4 HOH A 93 793 44 HOH HOH . 
F 4 HOH A 94 794 77 HOH HOH . 
F 4 HOH A 95 795 137 HOH HOH . 
F 4 HOH A 96 796 17 HOH HOH . 
F 4 HOH A 97 797 72 HOH HOH . 
F 4 HOH A 98 798 5 HOH HOH . 
F 4 HOH A 99 799 90 HOH HOH . 
F 4 HOH A 100 800 149 HOH HOH . 
F 4 HOH A 101 801 69 HOH HOH . 
F 4 HOH A 102 802 130 HOH HOH . 
F 4 HOH A 103 803 119 HOH HOH . 
F 4 HOH A 104 804 11 HOH HOH . 
F 4 HOH A 105 805 20 HOH HOH . 
F 4 HOH A 106 806 74 HOH HOH . 
F 4 HOH A 107 807 47 HOH HOH . 
F 4 HOH A 108 808 3 HOH HOH . 
F 4 HOH A 109 809 54 HOH HOH . 
F 4 HOH A 110 810 29 HOH HOH . 
F 4 HOH A 111 811 4 HOH HOH . 
F 4 HOH A 112 812 155 HOH HOH . 
F 4 HOH A 113 813 82 HOH HOH . 
F 4 HOH A 114 814 153 HOH HOH . 
F 4 HOH A 115 815 43 HOH HOH . 
F 4 HOH A 116 816 16 HOH HOH . 
F 4 HOH A 117 817 40 HOH HOH . 
F 4 HOH A 118 818 98 HOH HOH . 
F 4 HOH A 119 819 21 HOH HOH . 
F 4 HOH A 120 820 99 HOH HOH . 
F 4 HOH A 121 821 45 HOH HOH . 
F 4 HOH A 122 822 46 HOH HOH . 
F 4 HOH A 123 823 150 HOH HOH . 
F 4 HOH A 124 824 163 HOH HOH . 
F 4 HOH A 125 825 101 HOH HOH . 
F 4 HOH A 126 826 122 HOH HOH . 
F 4 HOH A 127 827 94 HOH HOH . 
F 4 HOH A 128 828 85 HOH HOH . 
F 4 HOH A 129 829 27 HOH HOH . 
F 4 HOH A 130 830 115 HOH HOH . 
F 4 HOH A 131 831 12 HOH HOH . 
F 4 HOH A 132 832 78 HOH HOH . 
F 4 HOH A 133 833 50 HOH HOH . 
F 4 HOH A 134 834 132 HOH HOH . 
F 4 HOH A 135 835 38 HOH HOH . 
F 4 HOH A 136 836 30 HOH HOH . 
F 4 HOH A 137 837 86 HOH HOH . 
F 4 HOH A 138 838 36 HOH HOH . 
F 4 HOH A 139 839 91 HOH HOH . 
F 4 HOH A 140 840 114 HOH HOH . 
F 4 HOH A 141 841 161 HOH HOH . 
F 4 HOH A 142 842 80 HOH HOH . 
F 4 HOH A 143 843 105 HOH HOH . 
F 4 HOH A 144 844 165 HOH HOH . 
F 4 HOH A 145 845 41 HOH HOH . 
F 4 HOH A 146 846 67 HOH HOH . 
F 4 HOH A 147 847 138 HOH HOH . 
F 4 HOH A 148 848 162 HOH HOH . 
F 4 HOH A 149 849 145 HOH HOH . 
F 4 HOH A 150 850 112 HOH HOH . 
F 4 HOH A 151 851 51 HOH HOH . 
F 4 HOH A 152 852 134 HOH HOH . 
F 4 HOH A 153 853 143 HOH HOH . 
F 4 HOH A 154 854 140 HOH HOH . 
F 4 HOH A 155 855 158 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 . . . D 3 -22.305 14.747 -9.59 1 44.7 ? C1 GOL 603 A 1 
HETATM 2 O O1 GOL . . . D 3 -22.896 15.369 -8.458 1 42.3 ? O1 GOL 603 A 1 
HETATM 3 C C2 GOL . . . D 3 -20.983 14.05 -9.329 1 50.41 ? C2 GOL 603 A 1 
HETATM 4 O O2 GOL . . . D 3 -19.93 14.6 -10.062 1 50.99 ? O2 GOL 603 A 1 
HETATM 5 C C3 GOL . . . D 3 -20.596 13.949 -7.882 1 45.12 ? C3 GOL 603 A 1 
HETATM 6 O O3 GOL . . . D 3 -19.206 13.709 -7.732 1 40.04 ? O3 GOL 603 A 1 
HETATM 7 H H11 GOL . . . D 3 -22.158 15.491 -10.368 1 53.64 ? H11 GOL 603 A 1 
HETATM 8 H H12 GOL . . . D 3 -23.001 14.006 -9.977 1 53.64 ? H12 GOL 603 A 1 
HETATM 9 H HO1 GOL . . . D 3 -23.539 14.776 -8.059 1 50.76 ? HO1 GOL 603 A 1 
HETATM 10 H H2 GOL . . . D 3 -21.11 13.021 -9.683 1 60.49 ? H2 GOL 603 A 1 
HETATM 11 H HO2 GOL . . . D 3 -19.438 13.889 -10.483 1 61.19 ? HO2 GOL 603 A 1 
HETATM 12 H H31 GOL . . . D 3 -20.859 14.877 -7.379 1 54.15 ? H31 GOL 603 A 1 
HETATM 13 H H32 GOL . . . D 3 -21.163 13.143 -7.421 1 54.15 ? H32 GOL 603 A 1 
HETATM 14 H HO3 GOL . . . D 3 -19.071 12.857 -7.314 1 48.05 ? HO3 GOL 603 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           247 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#