data_5LYG
#
_model_server_result.job_id            Ik2MwryxcVQVAV7FdfiV9A 
_model_server_result.datetime_utc      '2024-12-24 16:56:18' 
_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          5lyg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":604}' 
#
_entry.id    5LYG 
#
_exptl.entry_id    5LYG 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              102.046 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONATE 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         90 
_cell.entry_id            5LYG 
_cell.length_a            45.73 
_cell.length_b            127.22 
_cell.length_c            39.38 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LYG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
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_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C3 H2 O4 -2' 
_chem_comp.formula_weight    102.046 
_chem_comp.id                MLI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MALONATE ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 C2 MLI sing 246 n n 
C1 C3 MLI sing 247 n n 
C1 H11 MLI sing 248 n n 
C1 H12 MLI sing 249 n n 
C2 O6 MLI doub 250 n n 
C2 O7 MLI sing 251 n n 
C3 O8 MLI doub 252 n n 
C3 O9 MLI sing 253 n n 
#
_atom_sites.entry_id                     5LYG 
_atom_sites.fract_transf_matrix[1][1]    0.021867 
_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]    0.00786 
_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]    0.025394 
_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 EDO A 1 601 1 EDO EDO . 
C 2 EDO A 1 602 2 EDO EDO . 
D 2 EDO A 1 603 3 EDO EDO . 
E 3 MLI A 1 604 1 MLI MLI . 
F 4 HOH A 1 701 9 HOH HOH . 
F 4 HOH A 2 702 5 HOH HOH . 
F 4 HOH A 3 703 18 HOH HOH . 
F 4 HOH A 4 704 121 HOH HOH . 
F 4 HOH A 5 705 16 HOH HOH . 
F 4 HOH A 6 706 41 HOH HOH . 
F 4 HOH A 7 707 8 HOH HOH . 
F 4 HOH A 8 708 65 HOH HOH . 
F 4 HOH A 9 709 58 HOH HOH . 
F 4 HOH A 10 710 24 HOH HOH . 
F 4 HOH A 11 711 72 HOH HOH . 
F 4 HOH A 12 712 34 HOH HOH . 
F 4 HOH A 13 713 82 HOH HOH . 
F 4 HOH A 14 714 37 HOH HOH . 
F 4 HOH A 15 715 7 HOH HOH . 
F 4 HOH A 16 716 88 HOH HOH . 
F 4 HOH A 17 717 3 HOH HOH . 
F 4 HOH A 18 718 81 HOH HOH . 
F 4 HOH A 19 719 105 HOH HOH . 
F 4 HOH A 20 720 20 HOH HOH . 
F 4 HOH A 21 721 21 HOH HOH . 
F 4 HOH A 22 722 10 HOH HOH . 
F 4 HOH A 23 723 22 HOH HOH . 
F 4 HOH A 24 724 6 HOH HOH . 
F 4 HOH A 25 725 127 HOH HOH . 
F 4 HOH A 26 726 44 HOH HOH . 
F 4 HOH A 27 727 118 HOH HOH . 
F 4 HOH A 28 728 80 HOH HOH . 
F 4 HOH A 29 729 43 HOH HOH . 
F 4 HOH A 30 730 4 HOH HOH . 
F 4 HOH A 31 731 49 HOH HOH . 
F 4 HOH A 32 732 122 HOH HOH . 
F 4 HOH A 33 733 73 HOH HOH . 
F 4 HOH A 34 734 2 HOH HOH . 
F 4 HOH A 35 735 107 HOH HOH . 
F 4 HOH A 36 736 92 HOH HOH . 
F 4 HOH A 37 737 46 HOH HOH . 
F 4 HOH A 38 738 54 HOH HOH . 
F 4 HOH A 39 739 63 HOH HOH . 
F 4 HOH A 40 740 94 HOH HOH . 
F 4 HOH A 41 741 57 HOH HOH . 
F 4 HOH A 42 742 29 HOH HOH . 
F 4 HOH A 43 743 61 HOH HOH . 
F 4 HOH A 44 744 25 HOH HOH . 
F 4 HOH A 45 745 33 HOH HOH . 
F 4 HOH A 46 746 69 HOH HOH . 
F 4 HOH A 47 747 13 HOH HOH . 
F 4 HOH A 48 748 101 HOH HOH . 
F 4 HOH A 49 749 36 HOH HOH . 
F 4 HOH A 50 750 30 HOH HOH . 
F 4 HOH A 51 751 14 HOH HOH . 
F 4 HOH A 52 752 68 HOH HOH . 
F 4 HOH A 53 753 47 HOH HOH . 
F 4 HOH A 54 754 26 HOH HOH . 
F 4 HOH A 55 755 79 HOH HOH . 
F 4 HOH A 56 756 23 HOH HOH . 
F 4 HOH A 57 757 108 HOH HOH . 
F 4 HOH A 58 758 39 HOH HOH . 
F 4 HOH A 59 759 67 HOH HOH . 
F 4 HOH A 60 760 17 HOH HOH . 
F 4 HOH A 61 761 62 HOH HOH . 
F 4 HOH A 62 762 66 HOH HOH . 
F 4 HOH A 63 763 91 HOH HOH . 
F 4 HOH A 64 764 19 HOH HOH . 
F 4 HOH A 65 765 77 HOH HOH . 
F 4 HOH A 66 766 109 HOH HOH . 
F 4 HOH A 67 767 1 HOH HOH . 
F 4 HOH A 68 768 38 HOH HOH . 
F 4 HOH A 69 769 112 HOH HOH . 
F 4 HOH A 70 770 12 HOH HOH . 
F 4 HOH A 71 771 27 HOH HOH . 
F 4 HOH A 72 772 11 HOH HOH . 
F 4 HOH A 73 773 40 HOH HOH . 
F 4 HOH A 74 774 120 HOH HOH . 
F 4 HOH A 75 775 89 HOH HOH . 
F 4 HOH A 76 776 56 HOH HOH . 
F 4 HOH A 77 777 110 HOH HOH . 
F 4 HOH A 78 778 35 HOH HOH . 
F 4 HOH A 79 779 53 HOH HOH . 
F 4 HOH A 80 780 64 HOH HOH . 
F 4 HOH A 81 781 98 HOH HOH . 
F 4 HOH A 82 782 42 HOH HOH . 
F 4 HOH A 83 783 75 HOH HOH . 
F 4 HOH A 84 784 76 HOH HOH . 
F 4 HOH A 85 785 100 HOH HOH . 
F 4 HOH A 86 786 32 HOH HOH . 
F 4 HOH A 87 787 31 HOH HOH . 
F 4 HOH A 88 788 125 HOH HOH . 
F 4 HOH A 89 789 55 HOH HOH . 
F 4 HOH A 90 790 126 HOH HOH . 
F 4 HOH A 91 791 28 HOH HOH . 
F 4 HOH A 92 792 96 HOH HOH . 
F 4 HOH A 93 793 113 HOH HOH . 
F 4 HOH A 94 794 60 HOH HOH . 
F 4 HOH A 95 795 116 HOH HOH . 
F 4 HOH A 96 796 104 HOH HOH . 
F 4 HOH A 97 797 93 HOH HOH . 
F 4 HOH A 98 798 71 HOH HOH . 
F 4 HOH A 99 799 114 HOH HOH . 
F 4 HOH A 100 800 95 HOH HOH . 
F 4 HOH A 101 801 48 HOH HOH . 
F 4 HOH A 102 802 123 HOH HOH . 
F 4 HOH A 103 803 83 HOH HOH . 
F 4 HOH A 104 804 84 HOH HOH . 
F 4 HOH A 105 805 106 HOH HOH . 
F 4 HOH A 106 806 50 HOH HOH . 
F 4 HOH A 107 807 97 HOH HOH . 
F 4 HOH A 108 808 45 HOH HOH . 
F 4 HOH A 109 809 115 HOH HOH . 
F 4 HOH A 110 810 87 HOH HOH . 
F 4 HOH A 111 811 51 HOH HOH . 
F 4 HOH A 112 812 59 HOH HOH . 
F 4 HOH A 113 813 117 HOH HOH . 
F 4 HOH A 114 814 86 HOH HOH . 
F 4 HOH A 115 815 103 HOH HOH . 
F 4 HOH A 116 816 78 HOH HOH . 
F 4 HOH A 117 817 119 HOH HOH . 
F 4 HOH A 118 818 102 HOH HOH . 
F 4 HOH A 119 819 111 HOH HOH . 
F 4 HOH A 120 820 15 HOH HOH . 
F 4 HOH A 121 821 99 HOH HOH . 
F 4 HOH A 122 822 74 HOH HOH . 
F 4 HOH A 123 823 90 HOH HOH . 
F 4 HOH A 124 824 70 HOH HOH . 
F 4 HOH A 125 825 85 HOH HOH . 
F 4 HOH A 126 826 124 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 MLI . . . E 3 0.626 21.351 22.074 0.85 22.66 ? C1 MLI 604 A 1 
HETATM 2 C C2 MLI . . . E 3 1.968 20.974 21.492 0.85 22.8 ? C2 MLI 604 A 1 
HETATM 3 C C3 MLI . . . E 3 -0.285 20.145 22.139 0.85 23.43 ? C3 MLI 604 A 1 
HETATM 4 O O6 MLI . . . E 3 2.092 20.918 20.25 0.85 23.75 ? O6 MLI 604 A 1 
HETATM 5 O O7 MLI . . . E 3 2.91 20.732 22.278 0.85 23 ? O7 MLI 604 A 1 
HETATM 6 O O8 MLI . . . E 3 -1.52 20.34 22.143 0.85 27.16 ? O8 MLI 604 A 1 
HETATM 7 O O9 MLI . . . E 3 0.215 19.001 22.189 0.85 24.92 ? O9 MLI 604 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           335 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           7 
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