data_1VCG # _model_server_result.job_id iI5Sae3x2cytTZGdYPEPrA _model_server_result.datetime_utc '2025-01-27 04:49:38' _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 1vcg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":504}' # _entry.id 1VCG # _exptl.entry_id 1VCG _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 4 _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 1VCG _cell.length_a 112.953 _cell.length_b 112.953 _cell.length_c 261.283 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VCG _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS octameric 8 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1,2 A,B,C,D,E,F,G,H 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 covale ? covale1 A C ALA 65 A ALA 65 1_555 A N MSE 66 A MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 A C MSE 66 A MSE 66 1_555 A N THR 67 A THR 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C GLY 90 A GLY 90 1_555 A N MSE 91 A MSE 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 A C MSE 91 A MSE 91 1_555 A N MSE 92 A MSE 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 A C MSE 92 A MSE 92 1_555 A N LEU 93 A LEU 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale6 A C GLU 142 A GLU 142 1_555 A N MSE 143 A MSE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale7 A C MSE 143 A MSE 143 1_555 A N LEU 144 A LEU 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 A C VAL 184 A VAL 184 1_555 A N MSE 185 A MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale9 A C MSE 185 A MSE 185 1_555 A N VAL 186 A VAL 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 B C ALA 65 B ALA 65 1_555 B N MSE 66 B MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale11 B C MSE 66 B MSE 66 1_555 B N THR 67 B THR 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 B C GLY 90 B GLY 90 1_555 B N MSE 91 B MSE 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 B C MSE 91 B MSE 91 1_555 B N MSE 92 B MSE 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale14 B C MSE 92 B MSE 92 1_555 B N LEU 93 B LEU 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale15 B C GLU 142 B GLU 142 1_555 B N MSE 143 B MSE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale16 B C MSE 143 B MSE 143 1_555 B N LEU 144 B LEU 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale17 B C VAL 184 B VAL 184 1_555 B N MSE 185 B MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale18 B C MSE 185 B MSE 185 1_555 B N VAL 186 B VAL 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale19 C C ALA 65 C ALA 65 1_555 C N MSE 66 C MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale20 C C MSE 66 C MSE 66 1_555 C N THR 67 C THR 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale21 C C GLY 90 C GLY 90 1_555 C N MSE 91 C MSE 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale22 C C MSE 91 C MSE 91 1_555 C N MSE 92 C MSE 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale23 C C MSE 92 C MSE 92 1_555 C N LEU 93 C LEU 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale24 C C GLU 142 C GLU 142 1_555 C N MSE 143 C MSE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale25 C C MSE 143 C MSE 143 1_555 C N LEU 144 C LEU 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale26 C C VAL 184 C VAL 184 1_555 C N MSE 185 C MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale27 C C MSE 185 C MSE 185 1_555 C N VAL 186 C VAL 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale28 D C ALA 65 D ALA 65 1_555 D N MSE 66 D MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale29 D C MSE 66 D MSE 66 1_555 D N THR 67 D THR 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale30 D C GLY 90 D GLY 90 1_555 D N MSE 91 D MSE 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale31 D C MSE 91 D MSE 91 1_555 D N MSE 92 D MSE 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale32 D C MSE 92 D MSE 92 1_555 D N LEU 93 D LEU 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale33 D C GLU 142 D GLU 142 1_555 D N MSE 143 D MSE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale34 D C MSE 143 D MSE 143 1_555 D N LEU 144 D LEU 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale35 D C VAL 184 D VAL 184 1_555 D N MSE 185 D MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale36 D C MSE 185 D MSE 185 1_555 D N VAL 186 D VAL 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _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 83 n n N1 C10 FMN doub 84 n n C2 O2 FMN doub 85 n n C2 N3 FMN sing 86 n n N3 C4 FMN sing 87 n n N3 HN3 FMN sing 88 n n C4 O4 FMN doub 89 n n C4 C4A FMN sing 90 n n C4A N5 FMN doub 91 n n C4A C10 FMN sing 92 n n N5 C5A FMN sing 93 n n C5A C6 FMN doub 94 n y C5A C9A FMN sing 95 n y C6 C7 FMN sing 96 n y C6 H6 FMN sing 97 n n C7 C7M FMN sing 98 n n C7 C8 FMN doub 99 n y C7M HM71 FMN sing 100 n n C7M HM72 FMN sing 101 n n C7M HM73 FMN sing 102 n n C8 C8M FMN sing 103 n n C8 C9 FMN sing 104 n y C8M HM81 FMN sing 105 n n C8M HM82 FMN sing 106 n n C8M HM83 FMN sing 107 n n C9 C9A FMN doub 108 n y C9 H9 FMN sing 109 n n C9A N10 FMN sing 110 n n N10 C10 FMN sing 111 n n N10 C1' FMN sing 112 n n C1' C2' FMN sing 113 n n C1' "H1'1" FMN sing 114 n n C1' "H1'2" FMN sing 115 n n C2' O2' FMN sing 116 n n C2' C3' FMN sing 117 n n C2' H2' FMN sing 118 n n O2' HO2' FMN sing 119 n n C3' O3' FMN sing 120 n n C3' C4' FMN sing 121 n n C3' H3' FMN sing 122 n n O3' HO3' FMN sing 123 n n C4' O4' FMN sing 124 n n C4' C5' FMN sing 125 n n C4' H4' FMN sing 126 n n O4' HO4' FMN sing 127 n n C5' O5' FMN sing 128 n n C5' "H5'1" FMN sing 129 n n C5' "H5'2" FMN sing 130 n n O5' P FMN sing 131 n n P O1P FMN doub 132 n n P O2P FMN sing 133 n n P O3P FMN sing 134 n n O2P HOP2 FMN sing 135 n n O3P HOP3 FMN sing 136 n n # _atom_sites.entry_id 1VCG _atom_sites.fract_transf_matrix[1][1] 0.008853 _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] 0.008853 _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] 0.003827 _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 E 2 FMN A 1 501 501 FMN FMN . F 2 FMN B 1 502 502 FMN FMN . G 2 FMN C 1 503 503 FMN FMN . H 2 FMN D 1 504 504 FMN FMN . # 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 . . . H 2 46.681 32.456 22.869 1 92.96 ? N1 FMN 504 D 1 HETATM 2 C C2 FMN . . . H 2 45.846 31.641 23.536 1 92.53 ? C2 FMN 504 D 1 HETATM 3 O O2 FMN . . . H 2 45.295 31.831 24.62 1 91.77 ? O2 FMN 504 D 1 HETATM 4 N N3 FMN . . . H 2 45.523 30.337 22.925 1 93.1 ? N3 FMN 504 D 1 HETATM 5 C C4 FMN . . . H 2 46.066 29.914 21.663 1 93.52 ? C4 FMN 504 D 1 HETATM 6 O O4 FMN . . . H 2 45.69 28.784 21.294 1 93.56 ? O4 FMN 504 D 1 HETATM 7 C C4A FMN . . . H 2 46.927 30.805 21.038 1 93.26 ? C4A FMN 504 D 1 HETATM 8 N N5 FMN . . . H 2 47.448 30.455 19.901 1 93.37 ? N5 FMN 504 D 1 HETATM 9 C C5A FMN . . . H 2 48.35 31.319 19.218 1 93.43 ? C5A FMN 504 D 1 HETATM 10 C C6 FMN . . . H 2 48.957 30.966 17.971 1 93.41 ? C6 FMN 504 D 1 HETATM 11 C C7 FMN . . . H 2 49.882 31.877 17.314 1 93.67 ? C7 FMN 504 D 1 HETATM 12 C C7M FMN . . . H 2 50.358 31.221 16.02 1 93.13 ? C7M FMN 504 D 1 HETATM 13 C C8 FMN . . . H 2 50.205 33.181 17.924 1 93.39 ? C8 FMN 504 D 1 HETATM 14 C C8M FMN . . . H 2 51.146 34.08 17.236 1 93.1 ? C8M FMN 504 D 1 HETATM 15 C C9 FMN . . . H 2 49.617 33.548 19.142 1 93.27 ? C9 FMN 504 D 1 HETATM 16 C C9A FMN . . . H 2 48.656 32.642 19.865 1 92.9 ? C9A FMN 504 D 1 HETATM 17 N N10 FMN . . . H 2 48.103 33.06 21.086 1 91.51 ? N10 FMN 504 D 1 HETATM 18 C C10 FMN . . . H 2 47.253 32.164 21.684 1 92.57 ? C10 FMN 504 D 1 HETATM 19 C C1' FMN . . . H 2 48.293 34.311 21.821 1 87.78 ? C1' FMN 504 D 1 HETATM 20 C C2' FMN . . . H 2 49.539 34.556 22.642 1 84.17 ? C2' FMN 504 D 1 HETATM 21 O O2' FMN . . . H 2 49.68 33.572 23.631 1 83.59 ? O2' FMN 504 D 1 HETATM 22 C C3' FMN . . . H 2 49.355 35.931 23.254 1 81.91 ? C3' FMN 504 D 1 HETATM 23 O O3' FMN . . . H 2 48.095 36.542 22.853 1 82.28 ? O3' FMN 504 D 1 HETATM 24 C C4' FMN . . . H 2 50.362 37.035 22.911 1 79.08 ? C4' FMN 504 D 1 HETATM 25 O O4' FMN . . . H 2 50.02 38.23 23.559 1 80.5 ? O4' FMN 504 D 1 HETATM 26 C C5' FMN . . . H 2 50.628 37.335 21.403 1 73.52 ? C5' FMN 504 D 1 HETATM 27 O O5' FMN . . . H 2 52.068 37.2 21.374 1 67.74 ? O5' FMN 504 D 1 HETATM 28 P P FMN . . . H 2 52.926 38.442 21.738 1 62.8 ? P FMN 504 D 1 HETATM 29 O O1P FMN . . . H 2 54.453 38.348 21.805 1 61.77 ? O1P FMN 504 D 1 HETATM 30 O O2P FMN . . . H 2 52.298 39.778 21.483 1 62.22 ? O2P FMN 504 D 1 HETATM 31 O O3P FMN . . . H 2 53.216 38.366 20.243 1 62.24 ? O3P FMN 504 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #