data_5DKK # _model_server_result.job_id GybkgxQRadbE748xbHogLQ _model_server_result.datetime_utc '2024-11-08 09:14:19' _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 5dkk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5DKK # _exptl.entry_id 5DKK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 456.344 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FLAVIN MONONUCLEOTIDE' _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 5DKK _cell.length_a 64.37 _cell.length_b 69.21 _cell.length_c 74.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DKK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,H 1 1 B,G,I 2 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 ? 2 C N N ? 2 G N N # _chem_comp.formula 'C17 H21 N4 O9 P' _chem_comp.formula_weight 456.344 _chem_comp.id FMN _chem_comp.mon_nstd_flag . _chem_comp.name 'FLAVIN MONONUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVIN MONOPHOSPHATE' # 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 N1 C2 FMN sing 98 n n N1 C10 FMN doub 99 n n C2 O2 FMN doub 100 n n C2 N3 FMN sing 101 n n N3 C4 FMN sing 102 n n N3 HN3 FMN sing 103 n n C4 O4 FMN doub 104 n n C4 C4A FMN sing 105 n n C4A N5 FMN doub 106 n n C4A C10 FMN sing 107 n n N5 C5A FMN sing 108 n n C5A C6 FMN doub 109 n y C5A C9A FMN sing 110 n y C6 C7 FMN sing 111 n y C6 H6 FMN sing 112 n n C7 C7M FMN sing 113 n n C7 C8 FMN doub 114 n y C7M HM71 FMN sing 115 n n C7M HM72 FMN sing 116 n n C7M HM73 FMN sing 117 n n C8 C8M FMN sing 118 n n C8 C9 FMN sing 119 n y C8M HM81 FMN sing 120 n n C8M HM82 FMN sing 121 n n C8M HM83 FMN sing 122 n n C9 C9A FMN doub 123 n y C9 H9 FMN sing 124 n n C9A N10 FMN sing 125 n n N10 C10 FMN sing 126 n n N10 C1' FMN sing 127 n n C1' C2' FMN sing 128 n n C1' "H1'1" FMN sing 129 n n C1' "H1'2" FMN sing 130 n n C2' O2' FMN sing 131 n n C2' C3' FMN sing 132 n n C2' H2' FMN sing 133 n n O2' HO2' FMN sing 134 n n C3' O3' FMN sing 135 n n C3' C4' FMN sing 136 n n C3' H3' FMN sing 137 n n O3' HO3' FMN sing 138 n n C4' O4' FMN sing 139 n n C4' C5' FMN sing 140 n n C4' H4' FMN sing 141 n n O4' HO4' FMN sing 142 n n C5' O5' FMN sing 143 n n C5' "H5'1" FMN sing 144 n n C5' "H5'2" FMN sing 145 n n O5' P FMN sing 146 n n P O1P FMN doub 147 n n P O2P FMN sing 148 n n P O3P FMN sing 149 n n O2P HOP2 FMN sing 150 n n O3P HOP3 FMN sing 151 n n # _atom_sites.entry_id 5DKK _atom_sites.fract_transf_matrix[1][1] 0.015535 _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] 0.014449 _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] 0.013405 _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 2 FMN A 1 401 500 FMN FMN . D 3 ACT A 1 402 1 ACT ACT . E 3 ACT A 1 403 4 ACT ACT . F 4 EDO A 1 404 1 EDO EDO . G 2 FMN B 1 500 500 FMN FMN . H 5 HOH A 1 501 60 HOH HOH . H 5 HOH A 2 502 34 HOH HOH . H 5 HOH A 3 503 3 HOH HOH . H 5 HOH A 4 504 73 HOH HOH . H 5 HOH A 5 505 47 HOH HOH . H 5 HOH A 6 506 63 HOH HOH . H 5 HOH A 7 507 42 HOH HOH . H 5 HOH A 8 508 36 HOH HOH . H 5 HOH A 9 509 76 HOH HOH . H 5 HOH A 10 510 11 HOH HOH . H 5 HOH A 11 511 44 HOH HOH . H 5 HOH A 12 512 59 HOH HOH . H 5 HOH A 13 513 32 HOH HOH . H 5 HOH A 14 514 8 HOH HOH . H 5 HOH A 15 515 21 HOH HOH . H 5 HOH A 16 516 40 HOH HOH . H 5 HOH A 17 517 80 HOH HOH . H 5 HOH A 18 518 66 HOH HOH . H 5 HOH A 19 519 10 HOH HOH . H 5 HOH A 20 520 61 HOH HOH . H 5 HOH A 21 521 33 HOH HOH . H 5 HOH A 22 522 22 HOH HOH . H 5 HOH A 23 523 53 HOH HOH . H 5 HOH A 24 524 65 HOH HOH . H 5 HOH A 25 525 16 HOH HOH . I 5 HOH B 1 601 35 HOH HOH . I 5 HOH B 2 602 28 HOH HOH . I 5 HOH B 3 603 9 HOH HOH . I 5 HOH B 4 604 18 HOH HOH . I 5 HOH B 5 605 20 HOH HOH . I 5 HOH B 6 606 69 HOH HOH . I 5 HOH B 7 607 77 HOH HOH . I 5 HOH B 8 608 58 HOH HOH . I 5 HOH B 9 609 24 HOH HOH . I 5 HOH B 10 610 75 HOH HOH . I 5 HOH B 11 611 41 HOH HOH . I 5 HOH B 12 612 17 HOH HOH . I 5 HOH B 13 613 6 HOH HOH . I 5 HOH B 14 614 26 HOH HOH . I 5 HOH B 15 615 78 HOH HOH . I 5 HOH B 16 616 43 HOH HOH . I 5 HOH B 17 617 39 HOH HOH . I 5 HOH B 18 618 62 HOH HOH . I 5 HOH B 19 619 5 HOH HOH . I 5 HOH B 20 620 45 HOH HOH . I 5 HOH B 21 621 54 HOH HOH . I 5 HOH B 22 622 4 HOH HOH . I 5 HOH B 23 623 46 HOH HOH . I 5 HOH B 24 624 79 HOH HOH . I 5 HOH B 25 625 56 HOH HOH . I 5 HOH B 26 626 52 HOH HOH . I 5 HOH B 27 627 67 HOH HOH . I 5 HOH B 28 628 15 HOH HOH . I 5 HOH B 29 629 14 HOH HOH . I 5 HOH B 30 630 72 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 N N1 FMN . . . C 2 -0.143 25.952 -5.496 1 30.8 ? N1 FMN 401 A 1 HETATM 2 C C2 FMN . . . C 2 -0.278 25.073 -6.546 1 30.85 ? C2 FMN 401 A 1 HETATM 3 O O2 FMN . . . C 2 0.706 24.777 -7.214 1 32.05 ? O2 FMN 401 A 1 HETATM 4 N N3 FMN . . . C 2 -1.479 24.44 -6.791 1 30.37 ? N3 FMN 401 A 1 HETATM 5 C C4 FMN . . . C 2 -2.578 24.675 -5.996 1 31.14 ? C4 FMN 401 A 1 HETATM 6 O O4 FMN . . . C 2 -3.669 24.151 -6.278 1 31.29 ? O4 FMN 401 A 1 HETATM 7 C C4A FMN . . . C 2 -2.438 25.531 -4.903 1 32.91 ? C4A FMN 401 A 1 HETATM 8 N N5 FMN . . . C 2 -3.532 25.815 -4.107 1 32.51 ? N5 FMN 401 A 1 HETATM 9 C C5A FMN . . . C 2 -3.446 26.813 -3.151 1 36.21 ? C5A FMN 401 A 1 HETATM 10 C C6 FMN . . . C 2 -4.6 27.252 -2.506 1 29.61 ? C6 FMN 401 A 1 HETATM 11 C C7 FMN . . . C 2 -4.529 28.312 -1.62 1 30 ? C7 FMN 401 A 1 HETATM 12 C C7M FMN . . . C 2 -5.772 28.838 -0.966 1 27.97 ? C7M FMN 401 A 1 HETATM 13 C C8 FMN . . . C 2 -3.309 28.914 -1.354 1 30.83 ? C8 FMN 401 A 1 HETATM 14 C C8M FMN . . . C 2 -3.217 30.021 -0.352 1 29.38 ? C8M FMN 401 A 1 HETATM 15 C C9 FMN . . . C 2 -2.166 28.498 -2.011 1 33.39 ? C9 FMN 401 A 1 HETATM 16 C C9A FMN . . . C 2 -2.232 27.475 -2.946 1 35.94 ? C9A FMN 401 A 1 HETATM 17 N N10 FMN . . . C 2 -1.089 27.084 -3.631 1 35.5 ? N10 FMN 401 A 1 HETATM 18 C C10 FMN . . . C 2 -1.217 26.172 -4.663 1 34.53 ? C10 FMN 401 A 1 HETATM 19 C C1' FMN . . . C 2 0.155 27.933 -3.577 1 34.53 ? C1' FMN 401 A 1 HETATM 20 C C2' FMN . . . C 2 1.151 27.508 -2.498 1 34.86 ? C2' FMN 401 A 1 HETATM 21 O O2' FMN . . . C 2 0.476 27.175 -1.314 1 35.73 ? O2' FMN 401 A 1 HETATM 22 C C3' FMN . . . C 2 2.129 28.634 -2.179 1 38.29 ? C3' FMN 401 A 1 HETATM 23 O O3' FMN . . . C 2 1.383 29.75 -1.744 1 38.55 ? O3' FMN 401 A 1 HETATM 24 C C4' FMN . . . C 2 2.963 29.001 -3.408 1 39.82 ? C4' FMN 401 A 1 HETATM 25 O O4' FMN . . . C 2 3.817 27.927 -3.745 1 37.62 ? O4' FMN 401 A 1 HETATM 26 C C5' FMN . . . C 2 3.79 30.275 -3.208 1 43.83 ? C5' FMN 401 A 1 HETATM 27 O O5' FMN . . . C 2 4.313 30.372 -1.897 1 47.53 ? O5' FMN 401 A 1 HETATM 28 P P FMN . . . C 2 5.718 29.685 -1.466 1 54.26 ? P FMN 401 A 1 HETATM 29 O O1P FMN . . . C 2 6.855 30.249 -2.267 1 46.82 ? O1P FMN 401 A 1 HETATM 30 O O2P FMN . . . C 2 5.967 29.974 0.005 1 45.41 ? O2P FMN 401 A 1 HETATM 31 O O3P FMN . . . C 2 5.691 28.19 -1.73 1 46.52 ? O3P FMN 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 31 #