data_1VCF # _model_server_result.job_id ZSQH6684cC8ZdB755etWxg _model_server_result.datetime_utc '2025-01-27 04:36:42' _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 1vcf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 1VCF # _exptl.entry_id 1VCF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 456.344 _entity.id 3 _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 1VCF _cell.length_a 144.427 _cell.length_b 144.427 _cell.length_c 169.821 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VCF _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 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 ? octameric 8 author_defined_assembly 1 PISA,PQS tetrameric 4 software_defined_assembly 2 PISA,PQS tetrameric 4 software_defined_assembly 3 # 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 1 1,2,3,4 A,C,D 2 1,2,3,4 B,E 3 1,2,3,4 # 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' 2_755 -x+2,-y,z -1 0 0 0 -1 0 0 0 1 288.854 0 0 3 'crystal symmetry operation' 3_645 -y+1,x-1,z 0 -1 0 1 0 0 0 0 1 144.427 -144.427 0 4 'crystal symmetry operation' 4_665 y+1,-x+1,z 0 1 0 -1 0 0 0 0 1 144.427 144.427 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 covale ? covale1 A C ALA 65 A ALA 65 1_555 A N MSE 66 A MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MSE 66 A MSE 66 1_555 A N THR 67 A THR 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C MSE 92 A MSE 92 1_555 A N LEU 93 A LEU 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C GLU 142 A GLU 142 1_555 A N MSE 143 A MSE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale7 A C MSE 143 A MSE 143 1_555 A N LEU 144 A LEU 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 A C VAL 184 A VAL 184 1_555 A N MSE 185 A MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale11 B C MSE 66 B MSE 66 1_555 B N THR 67 B THR 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 B C GLY 90 B GLY 90 1_555 B N MSE 91 B MSE 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale16 B C MSE 143 B MSE 143 1_555 B N LEU 144 B LEU 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale17 B C VAL 184 B VAL 184 1_555 B N MSE 185 B MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale18 B C MSE 185 B MSE 185 1_555 B N VAL 186 B VAL 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OD1 ASP 135 A ASP 135 1_555 C CD CD . A CD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc2 A OD2 ASP 136 A ASP 136 1_555 C CD CD . A CD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 A OD1 ASP 136 A ASP 136 1_555 C CD CD . A CD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc4 C CD CD . A CD 601 1_555 B OD1 ASP 135 B ASP 135 13_645 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc5 C CD CD . A CD 601 1_555 B OD2 ASP 135 B ASP 135 13_645 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? # _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 1VCF _atom_sites.fract_transf_matrix[1][1] 0.006924 _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] 0.006924 _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] 0.005889 _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 CD A 1 601 601 CD CD . D 3 FMN A 1 501 501 FMN FMN . E 3 FMN B 1 502 502 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 . . . E 3 127.815 29.265 57.429 1 63.99 ? N1 FMN 502 B 1 HETATM 2 C C2 FMN . . . E 3 127.402 30.383 58.028 1 62.48 ? C2 FMN 502 B 1 HETATM 3 O O2 FMN . . . E 3 127.307 30.605 59.226 1 61.29 ? O2 FMN 502 B 1 HETATM 4 N N3 FMN . . . E 3 126.995 31.522 57.173 1 63.81 ? N3 FMN 502 B 1 HETATM 5 C C4 FMN . . . E 3 127.033 31.465 55.74 1 65.47 ? C4 FMN 502 B 1 HETATM 6 O O4 FMN . . . E 3 126.658 32.505 55.164 1 64.82 ? O4 FMN 502 B 1 HETATM 7 C C4A FMN . . . E 3 127.476 30.273 55.196 1 66.07 ? C4A FMN 502 B 1 HETATM 8 N N5 FMN . . . E 3 127.527 30.177 53.902 1 68.25 ? N5 FMN 502 B 1 HETATM 9 C C5A FMN . . . E 3 127.969 28.972 53.281 1 68.86 ? C5A FMN 502 B 1 HETATM 10 C C6 FMN . . . E 3 128.039 28.807 51.866 1 68.85 ? C6 FMN 502 B 1 HETATM 11 C C7 FMN . . . E 3 128.489 27.549 51.294 1 69.3 ? C7 FMN 502 B 1 HETATM 12 C C7M FMN . . . E 3 128.457 27.666 49.774 1 69.38 ? C7M FMN 502 B 1 HETATM 13 C C8 FMN . . . E 3 128.875 26.437 52.163 1 69.19 ? C8 FMN 502 B 1 HETATM 14 C C8M FMN . . . E 3 129.321 25.172 51.562 1 69.21 ? C8M FMN 502 B 1 HETATM 15 C C9 FMN . . . E 3 128.815 26.584 53.536 1 69.16 ? C9 FMN 502 B 1 HETATM 16 C C9A FMN . . . E 3 128.36 27.851 54.184 1 68.43 ? C9A FMN 502 B 1 HETATM 17 N N10 FMN . . . E 3 128.324 27.914 55.578 1 67.38 ? N10 FMN 502 B 1 HETATM 18 C C10 FMN . . . E 3 127.891 29.1 56.102 1 66.25 ? C10 FMN 502 B 1 HETATM 19 C C1' FMN . . . E 3 128.685 26.872 56.537 1 67.76 ? C1' FMN 502 B 1 HETATM 20 C C2' FMN . . . E 3 127.595 25.844 56.815 1 68.15 ? C2' FMN 502 B 1 HETATM 21 O O2' FMN . . . E 3 126.462 26.481 57.332 1 68.32 ? O2' FMN 502 B 1 HETATM 22 C C3' FMN . . . E 3 128.137 24.851 57.804 1 67.94 ? C3' FMN 502 B 1 HETATM 23 O O3' FMN . . . E 3 129.525 25.114 58.125 1 69.82 ? O3' FMN 502 B 1 HETATM 24 C C4' FMN . . . E 3 128.157 23.375 57.381 1 69.1 ? C4' FMN 502 B 1 HETATM 25 O O4' FMN . . . E 3 128.695 22.566 58.385 1 70.37 ? O4' FMN 502 B 1 HETATM 26 C C5' FMN . . . E 3 128.852 23.009 56.035 1 65.84 ? C5' FMN 502 B 1 HETATM 27 O O5' FMN . . . E 3 127.825 22.203 55.385 1 64.81 ? O5' FMN 502 B 1 HETATM 28 P P FMN . . . E 3 127.55 20.765 55.955 1 58.4 ? P FMN 502 B 1 HETATM 29 O O1P FMN . . . E 3 126.451 19.879 55.36 1 60.78 ? O1P FMN 502 B 1 HETATM 30 O O2P FMN . . . E 3 128.67 20.118 56.704 1 60.7 ? O2P FMN 502 B 1 HETATM 31 O O3P FMN . . . E 3 128.272 20.356 54.67 1 60.73 ? O3P FMN 502 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #