data_5LFA
#
_model_server_result.job_id            IKkYrzrdjCXg-iesIhXkEw 
_model_server_result.datetime_utc      '2024-11-15 03:43:07' 
_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          5lfa 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":602}' 
#
_entry.id    5LFA 
#
_exptl.entry_id    5LFA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              326.305 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol 
_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            5LFA 
_cell.length_a            56.183 
_cell.length_b            94.441 
_cell.length_c            103.579 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LFA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
_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,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                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 350 A CYS 350 1_555 D FE2 SF4 . A SF4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc2 A SG CYS 438 A CYS 438 1_555 D FE1 SF4 . A SF4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc3 A SG CYS 441 A CYS 441 1_555 D FE3 SF4 . A SF4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc4 A SG CYS 454 A CYS 454 1_555 D FE4 SF4 . A SF4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
#
_chem_comp.formula           'C13 H18 N4 O6' 
_chem_comp.formula_weight    326.305 
_chem_comp.id                DLZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "6,7-dimethyl-8-(1'-D-ribityl) lumazine" 
#
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 C7A DLZ sing 83 n n 
C7A C5A DLZ doub 84 n n 
C7A N8 DLZ sing 85 n n 
C5A C6 DLZ sing 86 n n 
C5A N5 DLZ sing 87 n n 
N5 C4A DLZ doub 88 n n 
C4A C4 DLZ sing 89 n n 
C4A C8 DLZ sing 90 n n 
C4 O4 DLZ doub 91 n n 
C4 N3 DLZ sing 92 n n 
N3 C2 DLZ sing 93 n n 
C2 O2 DLZ doub 94 n n 
C2 N1 DLZ sing 95 n n 
N1 C8 DLZ doub 96 n n 
C8 N8 DLZ sing 97 n n 
N8 C1' DLZ sing 98 n n 
C1' C2' DLZ sing 99 n n 
C2' O2' DLZ sing 100 n n 
C2' C3' DLZ sing 101 n n 
C3' O3' DLZ sing 102 n n 
C3' C4' DLZ sing 103 n n 
C4' O4' DLZ sing 104 n n 
C4' C5' DLZ sing 105 n n 
C5' O5' DLZ sing 106 n n 
C7 H7 DLZ sing 107 n n 
C7 H7A DLZ sing 108 n n 
C7 H7B DLZ sing 109 n n 
C6 H6 DLZ sing 110 n n 
C6 H6A DLZ sing 111 n n 
C6 H6B DLZ sing 112 n n 
N3 HN3 DLZ sing 113 n n 
C1' H1' DLZ sing 114 n n 
C1' "H1'A" DLZ sing 115 n n 
C2' H2' DLZ sing 116 n n 
O2' HO2' DLZ sing 117 n n 
C3' H3' DLZ sing 118 n n 
O3' HO3' DLZ sing 119 n n 
C4' H4' DLZ sing 120 n n 
O4' HO4' DLZ sing 121 n n 
C5' H5' DLZ sing 122 n n 
C5' "H5'A" DLZ sing 123 n n 
O5' HO5' DLZ sing 124 n n 
#
_atom_sites.entry_id                     5LFA 
_atom_sites.fract_transf_matrix[1][1]    0.017799 
_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]    0.010589 
_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]    0.009654 
_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 FAD A 1 601 1 FAD FAD . 
C 3 DLZ A 1 602 1 DLZ DLZ . 
D 4 SF4 A 1 603 1 SF4 SF4 . 
E 5 GOL A 1 604 1 GOL GOL . 
F 5 GOL A 1 605 3 GOL GOL . 
G 5 GOL A 1 606 4 GOL GOL . 
H 6 HOH A 1 701 110 HOH HOH . 
H 6 HOH A 2 702 67 HOH HOH . 
H 6 HOH A 3 703 27 HOH HOH . 
H 6 HOH A 4 704 16 HOH HOH . 
H 6 HOH A 5 705 61 HOH HOH . 
H 6 HOH A 6 706 37 HOH HOH . 
H 6 HOH A 7 707 39 HOH HOH . 
H 6 HOH A 8 708 34 HOH HOH . 
H 6 HOH A 9 709 32 HOH HOH . 
H 6 HOH A 10 710 116 HOH HOH . 
H 6 HOH A 11 711 108 HOH HOH . 
H 6 HOH A 12 712 87 HOH HOH . 
H 6 HOH A 13 713 23 HOH HOH . 
H 6 HOH A 14 714 72 HOH HOH . 
H 6 HOH A 15 715 26 HOH HOH . 
H 6 HOH A 16 716 46 HOH HOH . 
H 6 HOH A 17 717 111 HOH HOH . 
H 6 HOH A 18 718 80 HOH HOH . 
H 6 HOH A 19 719 11 HOH HOH . 
H 6 HOH A 20 720 49 HOH HOH . 
H 6 HOH A 21 721 126 HOH HOH . 
H 6 HOH A 22 722 74 HOH HOH . 
H 6 HOH A 23 723 109 HOH HOH . 
H 6 HOH A 24 724 59 HOH HOH . 
H 6 HOH A 25 725 17 HOH HOH . 
H 6 HOH A 26 726 5 HOH HOH . 
H 6 HOH A 27 727 101 HOH HOH . 
H 6 HOH A 28 728 107 HOH HOH . 
H 6 HOH A 29 729 35 HOH HOH . 
H 6 HOH A 30 730 2 HOH HOH . 
H 6 HOH A 31 731 70 HOH HOH . 
H 6 HOH A 32 732 12 HOH HOH . 
H 6 HOH A 33 733 115 HOH HOH . 
H 6 HOH A 34 734 66 HOH HOH . 
H 6 HOH A 35 735 58 HOH HOH . 
H 6 HOH A 36 736 94 HOH HOH . 
H 6 HOH A 37 737 36 HOH HOH . 
H 6 HOH A 38 738 22 HOH HOH . 
H 6 HOH A 39 739 114 HOH HOH . 
H 6 HOH A 40 740 117 HOH HOH . 
H 6 HOH A 41 741 18 HOH HOH . 
H 6 HOH A 42 742 21 HOH HOH . 
H 6 HOH A 43 743 10 HOH HOH . 
H 6 HOH A 44 744 63 HOH HOH . 
H 6 HOH A 45 745 1 HOH HOH . 
H 6 HOH A 46 746 92 HOH HOH . 
H 6 HOH A 47 747 24 HOH HOH . 
H 6 HOH A 48 748 77 HOH HOH . 
H 6 HOH A 49 749 100 HOH HOH . 
H 6 HOH A 50 750 50 HOH HOH . 
H 6 HOH A 51 751 31 HOH HOH . 
H 6 HOH A 52 752 62 HOH HOH . 
H 6 HOH A 53 753 75 HOH HOH . 
H 6 HOH A 54 754 85 HOH HOH . 
H 6 HOH A 55 755 88 HOH HOH . 
H 6 HOH A 56 756 14 HOH HOH . 
H 6 HOH A 57 757 79 HOH HOH . 
H 6 HOH A 58 758 73 HOH HOH . 
H 6 HOH A 59 759 19 HOH HOH . 
H 6 HOH A 60 760 40 HOH HOH . 
H 6 HOH A 61 761 53 HOH HOH . 
H 6 HOH A 62 762 57 HOH HOH . 
H 6 HOH A 63 763 54 HOH HOH . 
H 6 HOH A 64 764 121 HOH HOH . 
H 6 HOH A 65 765 45 HOH HOH . 
H 6 HOH A 66 766 78 HOH HOH . 
H 6 HOH A 67 767 13 HOH HOH . 
H 6 HOH A 68 768 60 HOH HOH . 
H 6 HOH A 69 769 103 HOH HOH . 
H 6 HOH A 70 770 65 HOH HOH . 
H 6 HOH A 71 771 20 HOH HOH . 
H 6 HOH A 72 772 113 HOH HOH . 
H 6 HOH A 73 773 112 HOH HOH . 
H 6 HOH A 74 774 52 HOH HOH . 
H 6 HOH A 75 775 102 HOH HOH . 
H 6 HOH A 76 776 76 HOH HOH . 
H 6 HOH A 77 777 25 HOH HOH . 
H 6 HOH A 78 778 51 HOH HOH . 
H 6 HOH A 79 779 56 HOH HOH . 
H 6 HOH A 80 780 91 HOH HOH . 
H 6 HOH A 81 781 83 HOH HOH . 
H 6 HOH A 82 782 71 HOH HOH . 
H 6 HOH A 83 783 124 HOH HOH . 
H 6 HOH A 84 784 125 HOH HOH . 
H 6 HOH A 85 785 106 HOH HOH . 
H 6 HOH A 86 786 64 HOH HOH . 
H 6 HOH A 87 787 29 HOH HOH . 
H 6 HOH A 88 788 33 HOH HOH . 
H 6 HOH A 89 789 86 HOH HOH . 
H 6 HOH A 90 790 42 HOH HOH . 
H 6 HOH A 91 791 118 HOH HOH . 
H 6 HOH A 92 792 15 HOH HOH . 
H 6 HOH A 93 793 68 HOH HOH . 
H 6 HOH A 94 794 93 HOH HOH . 
H 6 HOH A 95 795 55 HOH HOH . 
H 6 HOH A 96 796 47 HOH HOH . 
H 6 HOH A 97 797 84 HOH HOH . 
H 6 HOH A 98 798 44 HOH HOH . 
H 6 HOH A 99 799 6 HOH HOH . 
H 6 HOH A 100 800 99 HOH HOH . 
H 6 HOH A 101 801 81 HOH HOH . 
H 6 HOH A 102 802 48 HOH HOH . 
H 6 HOH A 103 803 69 HOH HOH . 
H 6 HOH A 104 804 123 HOH HOH . 
H 6 HOH A 105 805 95 HOH HOH . 
H 6 HOH A 106 806 105 HOH HOH . 
H 6 HOH A 107 807 122 HOH HOH . 
H 6 HOH A 108 808 82 HOH HOH . 
H 6 HOH A 109 809 119 HOH HOH . 
H 6 HOH A 110 810 97 HOH HOH . 
H 6 HOH A 111 811 120 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 DLZ . . . C 3 7.733 -31.662 11.026 1 26.12 ? C7 DLZ 602 A 1 
HETATM 2 C C7A DLZ . . . C 3 9.086 -32.143 11.518 1 27.03 ? C7A DLZ 602 A 1 
HETATM 3 C C5A DLZ . . . C 3 10.302 -31.27 11.352 1 27.73 ? C5A DLZ 602 A 1 
HETATM 4 C C6 DLZ . . . C 3 10.172 -29.908 10.705 1 27.56 ? C6 DLZ 602 A 1 
HETATM 5 N N5 DLZ . . . C 3 11.53 -31.697 11.789 1 27.2 ? N5 DLZ 602 A 1 
HETATM 6 C C4A DLZ . . . C 3 11.694 -32.927 12.377 1 28.72 ? C4A DLZ 602 A 1 
HETATM 7 C C4 DLZ . . . C 3 13.005 -33.469 12.873 1 30.08 ? C4 DLZ 602 A 1 
HETATM 8 O O4 DLZ . . . C 3 14.034 -32.772 12.739 1 33.26 ? O4 DLZ 602 A 1 
HETATM 9 N N3 DLZ . . . C 3 13.054 -34.708 13.457 1 29.07 ? N3 DLZ 602 A 1 
HETATM 10 C C2 DLZ . . . C 3 11.942 -35.471 13.6 1 26.14 ? C2 DLZ 602 A 1 
HETATM 11 O O2 DLZ . . . C 3 11.979 -36.604 14.133 1 27.86 ? O2 DLZ 602 A 1 
HETATM 12 N N1 DLZ . . . C 3 10.734 -35.039 13.182 1 24.7 ? N1 DLZ 602 A 1 
HETATM 13 C C8 DLZ . . . C 3 10.539 -33.836 12.58 1 27.17 ? C8 DLZ 602 A 1 
HETATM 14 N N8 DLZ . . . C 3 9.248 -33.424 12.149 1 28.24 ? N8 DLZ 602 A 1 
HETATM 15 C C1' DLZ . . . C 3 8.164 -34.401 12.327 1 28.6 ? C1' DLZ 602 A 1 
HETATM 16 C C2' DLZ . . . C 3 8.426 -35.465 11.233 1 28.43 ? C2' DLZ 602 A 1 
HETATM 17 O O2' DLZ . . . C 3 8.978 -34.892 10.049 1 24.52 ? O2' DLZ 602 A 1 
HETATM 18 C C3' DLZ . . . C 3 7.216 -36.224 10.745 1 30.85 ? C3' DLZ 602 A 1 
HETATM 19 O O3' DLZ . . . C 3 6.227 -35.304 10.316 1 32.58 ? O3' DLZ 602 A 1 
HETATM 20 C C4' DLZ . . . C 3 6.713 -37.101 11.855 1 35.57 ? C4' DLZ 602 A 1 
HETATM 21 O O4' DLZ . . . C 3 7.779 -38.002 12.167 1 39.59 ? O4' DLZ 602 A 1 
HETATM 22 C C5' DLZ . . . C 3 5.482 -37.888 11.444 1 39.07 ? C5' DLZ 602 A 1 
HETATM 23 O O5' DLZ . . . C 3 5.318 -38.996 12.343 1 39.26 ? O5' DLZ 602 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           23 
#