data_4D1Y # _model_server_result.job_id LBMaIl1TU7HlHT4jl3jBMw _model_server_result.datetime_utc '2025-03-04 14:29:19' _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 4d1y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1176}' # _entry.id 4D1Y # _exptl.entry_id 4D1Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.364 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RIBOFLAVIN _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 108.34 _cell.angle_gamma 90 _cell.entry_id 4D1Y _cell.length_a 122.601 _cell.length_b 40.851 _cell.length_c 71.645 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D1Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 2 _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 99 A CYS 74 1_555 D ZN ZN . A ZN 1177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc2 A SG CYS 136 A CYS 111 1_555 D ZN ZN . A ZN 1177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 D ZN ZN . A ZN 1177 1_555 F O HOH . A HOH 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc4 B SG CYS 99 B CYS 74 1_555 E ZN ZN . B ZN 1176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc5 B SG CYS 136 B CYS 111 1_555 E ZN ZN . B ZN 1176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc6 E ZN ZN . B ZN 1176 1_555 G O HOH . B HOH 2016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? # _chem_comp.formula 'C17 H20 N4 O6' _chem_comp.formula_weight 376.364 _chem_comp.id RBF _chem_comp.mon_nstd_flag . _chem_comp.name RIBOFLAVIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVINE;VITAMIN B2' # 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 RBF sing 251 n n N1 C10 RBF doub 252 n n C2 O2 RBF doub 253 n n C2 N3 RBF sing 254 n n N3 C4 RBF sing 255 n n N3 HN3 RBF sing 256 n n C4 O4 RBF doub 257 n n C4 C4A RBF sing 258 n n C4A N5 RBF doub 259 n n C4A C10 RBF sing 260 n n N5 C5A RBF sing 261 n n C5A C6 RBF doub 262 n y C5A C9A RBF sing 263 n y C6 C7 RBF sing 264 n y C6 HC6 RBF sing 265 n n C7 C7M RBF sing 266 n n C7 C8 RBF doub 267 n y C7M HC71 RBF sing 268 n n C7M HC72 RBF sing 269 n n C7M HC73 RBF sing 270 n n C8 C8M RBF sing 271 n n C8 C9 RBF sing 272 n y C8M HC81 RBF sing 273 n n C8M HC82 RBF sing 274 n n C8M HC83 RBF sing 275 n n C9 C9A RBF doub 276 n y C9 HC9 RBF sing 277 n n C9A N10 RBF sing 278 n n N10 C10 RBF sing 279 n n N10 C1' RBF sing 280 n n C1' C2' RBF sing 281 n n C1' HC11 RBF sing 282 n n C1' HC12 RBF sing 283 n n C2' O2' RBF sing 284 n n C2' C3' RBF sing 285 n n C2' HC2' RBF sing 286 n n O2' HO2' RBF sing 287 n n C3' O3' RBF sing 288 n n C3' C4' RBF sing 289 n n C3' HC3' RBF sing 290 n n O3' HO3' RBF sing 291 n n C4' O4' RBF sing 292 n n C4' C5' RBF sing 293 n n C4' HC4' RBF sing 294 n n O4' HO4' RBF sing 295 n n C5' O5' RBF sing 296 n n C5' HC51 RBF sing 297 n n C5' HC52 RBF sing 298 n n O5' HO5' RBF sing 299 n n # _atom_sites.entry_id 4D1Y _atom_sites.fract_transf_matrix[1][1] 0.008157 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002704 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024479 _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] 0.014705 _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 RBF A 1 1176 1176 RBF RBF . D 3 ZN A 1 1177 1177 ZN ZN . E 3 ZN B 1 1176 1176 ZN ZN . F 4 HOH A 1 2001 2001 HOH HOH . F 4 HOH A 2 2002 2002 HOH HOH . F 4 HOH A 3 2003 2003 HOH HOH . F 4 HOH A 4 2004 2004 HOH HOH . F 4 HOH A 5 2005 2005 HOH HOH . F 4 HOH A 6 2006 2006 HOH HOH . F 4 HOH A 7 2007 2007 HOH HOH . F 4 HOH A 8 2008 2008 HOH HOH . F 4 HOH A 9 2009 2009 HOH HOH . F 4 HOH A 10 2010 2010 HOH HOH . F 4 HOH A 11 2011 2011 HOH HOH . F 4 HOH A 12 2012 2012 HOH HOH . F 4 HOH A 13 2013 2013 HOH HOH . F 4 HOH A 14 2014 2014 HOH HOH . F 4 HOH A 15 2015 2015 HOH HOH . F 4 HOH A 16 2016 2016 HOH HOH . F 4 HOH A 17 2017 2017 HOH HOH . F 4 HOH A 18 2018 2018 HOH HOH . F 4 HOH A 19 2019 2019 HOH HOH . F 4 HOH A 20 2020 2020 HOH HOH . F 4 HOH A 21 2021 2021 HOH HOH . F 4 HOH A 22 2022 2022 HOH HOH . F 4 HOH A 23 2023 2023 HOH HOH . F 4 HOH A 24 2024 2024 HOH HOH . F 4 HOH A 25 2025 2025 HOH HOH . F 4 HOH A 26 2026 2026 HOH HOH . F 4 HOH A 27 2027 2027 HOH HOH . F 4 HOH A 28 2028 2028 HOH HOH . F 4 HOH A 29 2029 2029 HOH HOH . F 4 HOH A 30 2030 2030 HOH HOH . F 4 HOH A 31 2031 2031 HOH HOH . F 4 HOH A 32 2032 2032 HOH HOH . F 4 HOH A 33 2033 2033 HOH HOH . F 4 HOH A 34 2034 2034 HOH HOH . F 4 HOH A 35 2035 2035 HOH HOH . F 4 HOH A 36 2036 2036 HOH HOH . F 4 HOH A 37 2037 2037 HOH HOH . G 4 HOH B 1 2001 2001 HOH HOH . G 4 HOH B 2 2002 2002 HOH HOH . G 4 HOH B 3 2003 2003 HOH HOH . G 4 HOH B 4 2004 2004 HOH HOH . G 4 HOH B 5 2005 2005 HOH HOH . G 4 HOH B 6 2006 2006 HOH HOH . G 4 HOH B 7 2007 2007 HOH HOH . G 4 HOH B 8 2008 2008 HOH HOH . G 4 HOH B 9 2009 2009 HOH HOH . G 4 HOH B 10 2010 2010 HOH HOH . G 4 HOH B 11 2011 2011 HOH HOH . G 4 HOH B 12 2012 2012 HOH HOH . G 4 HOH B 13 2013 2013 HOH HOH . G 4 HOH B 14 2014 2014 HOH HOH . G 4 HOH B 15 2015 2015 HOH HOH . G 4 HOH B 16 2016 2016 HOH HOH . G 4 HOH B 17 2017 2017 HOH HOH . G 4 HOH B 18 2018 2018 HOH HOH . G 4 HOH B 19 2019 2019 HOH HOH . G 4 HOH B 20 2020 2020 HOH HOH . G 4 HOH B 21 2021 2021 HOH HOH . G 4 HOH B 22 2022 2022 HOH HOH . G 4 HOH B 23 2023 2023 HOH HOH . G 4 HOH B 24 2024 2024 HOH HOH . G 4 HOH B 25 2025 2025 HOH HOH . G 4 HOH B 26 2026 2026 HOH HOH . G 4 HOH B 27 2027 2027 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 RBF . A . C 2 -35.043 -7.482 31.777 0.56 38.84 ? N1 RBF 1176 A 1 HETATM 2 N N1 RBF . B . C 2 -35.544 -4.358 27.026 0.44 40.03 ? N1 RBF 1176 A 1 HETATM 3 C C2 RBF . A . C 2 -35.209 -6.861 32.973 0.56 39.23 ? C2 RBF 1176 A 1 HETATM 4 C C2 RBF . B . C 2 -35.528 -5.011 25.835 0.44 40.84 ? C2 RBF 1176 A 1 HETATM 5 O O2 RBF . A . C 2 -35.013 -7.509 34.024 0.56 39.2 ? O2 RBF 1176 A 1 HETATM 6 O O2 RBF . B . C 2 -35.552 -4.343 24.778 0.44 40.31 ? O2 RBF 1176 A 1 HETATM 7 N N3 RBF . A . C 2 -35.571 -5.571 33.075 0.56 39.15 ? N3 RBF 1176 A 1 HETATM 8 N N3 RBF . B . C 2 -35.489 -6.352 25.745 0.44 39.79 ? N3 RBF 1176 A 1 HETATM 9 C C4 RBF . A . C 2 -35.797 -4.804 32.003 0.56 39.5 ? C4 RBF 1176 A 1 HETATM 10 C C4 RBF . B . C 2 -35.463 -7.141 26.825 0.44 40.51 ? C4 RBF 1176 A 1 HETATM 11 O O4 RBF . A . C 2 -36.136 -3.609 32.136 0.56 39.5 ? O4 RBF 1176 A 1 HETATM 12 O O4 RBF . B . C 2 -35.426 -8.385 26.706 0.44 40.09 ? O4 RBF 1176 A 1 HETATM 13 C C4A RBF . A . C 2 -35.643 -5.408 30.658 0.56 39.55 ? C4A RBF 1176 A 1 HETATM 14 C C4A RBF . B . C 2 -35.477 -6.507 28.166 0.44 39.54 ? C4A RBF 1176 A 1 HETATM 15 N N5 RBF . A . C 2 -35.857 -4.697 29.53 0.56 39.46 ? N5 RBF 1176 A 1 HETATM 16 N N5 RBF . B . C 2 -35.451 -7.237 29.303 0.44 39.95 ? N5 RBF 1176 A 1 HETATM 17 C C5A RBF . A . C 2 -35.711 -5.272 28.315 0.56 40.34 ? C5A RBF 1176 A 1 HETATM 18 C C5A RBF . B . C 2 -35.48 -6.632 30.512 0.44 39.08 ? C5A RBF 1176 A 1 HETATM 19 C C6 RBF . A . C 2 -35.944 -4.52 27.17 0.56 39.86 ? C6 RBF 1176 A 1 HETATM 20 C C6 RBF . B . C 2 -35.472 -7.404 31.667 0.44 39.11 ? C6 RBF 1176 A 1 HETATM 21 C C7 RBF . A . C 2 -35.798 -5.099 25.915 0.56 40.49 ? C7 RBF 1176 A 1 HETATM 22 C C7 RBF . B . C 2 -35.502 -6.792 32.915 0.44 40.25 ? C7 RBF 1176 A 1 HETATM 23 C C7M RBF . A . C 2 -36.051 -4.278 24.679 0.56 40.22 ? C7M RBF 1176 A 1 HETATM 24 C C7M RBF . B . C 2 -35.492 -7.635 34.163 0.44 39.16 ? C7M RBF 1176 A 1 HETATM 25 C C8 RBF . A . C 2 -35.392 -6.525 25.795 0.56 39.65 ? C8 RBF 1176 A 1 HETATM 26 C C8 RBF . B . C 2 -35.548 -5.309 33.017 0.44 39.04 ? C8 RBF 1176 A 1 HETATM 27 C C8M RBF . A . C 2 -35.236 -7.148 24.433 0.56 39.85 ? C8M RBF 1176 A 1 HETATM 28 C C8M RBF . B . C 2 -35.582 -4.646 34.369 0.44 38.95 ? C8M RBF 1176 A 1 HETATM 29 C C9 RBF . A . C 2 -35.159 -7.281 26.938 0.56 40.51 ? C9 RBF 1176 A 1 HETATM 30 C C9 RBF . B . C 2 -35.558 -4.533 31.863 0.44 39.4 ? C9 RBF 1176 A 1 HETATM 31 C C9A RBF . A . C 2 -35.305 -6.703 28.195 0.56 39.4 ? C9A RBF 1176 A 1 HETATM 32 C C9A RBF . B . C 2 -35.526 -5.145 30.615 0.44 39.91 ? C9A RBF 1176 A 1 HETATM 33 N N10 RBF . A . C 2 -35.084 -7.467 29.361 0.56 40.23 ? N10 RBF 1176 A 1 HETATM 34 N N10 RBF . B . C 2 -35.541 -4.365 29.441 0.44 39.59 ? N10 RBF 1176 A 1 HETATM 35 C C10 RBF . A . C 2 -35.238 -6.832 30.61 0.56 39.67 ? C10 RBF 1176 A 1 HETATM 36 C C10 RBF . B . C 2 -35.519 -5.027 28.199 0.44 40.17 ? C10 RBF 1176 A 1 HETATM 37 C C1' RBF . A . C 2 -34.669 -8.873 29.264 0.56 41.63 ? C1' RBF 1176 A 1 HETATM 38 C C1' RBF . B . C 2 -35.578 -2.902 29.522 0.44 40.07 ? C1' RBF 1176 A 1 HETATM 39 C C2' RBF . A . C 2 -35.747 -9.861 29.693 0.56 43.11 ? C2' RBF 1176 A 1 HETATM 40 C C2' RBF . B . C 2 -36.989 -2.389 29.265 0.44 41.06 ? C2' RBF 1176 A 1 HETATM 41 O O2' RBF . A . C 2 -35.974 -9.734 31.099 0.56 43.54 ? O2' RBF 1176 A 1 HETATM 42 O O2' RBF . B . C 2 -37.144 -2.134 27.864 0.44 41.67 ? O2' RBF 1176 A 1 HETATM 43 C C3' RBF . A . C 2 -35.293 -11.285 29.39 0.56 44.06 ? C3' RBF 1176 A 1 HETATM 44 C C3' RBF . B . C 2 -37.265 -1.107 30.042 0.44 41.47 ? C3' RBF 1176 A 1 HETATM 45 O O3' RBF . A . C 2 -34.577 -11.313 28.148 0.56 43.94 ? O3' RBF 1176 A 1 HETATM 46 O O3' RBF . B . C 2 -36.084 -0.692 30.738 0.44 41.36 ? O3' RBF 1176 A 1 HETATM 47 C C4' RBF . A . C 2 -36.468 -12.257 29.328 0.56 45.34 ? C4' RBF 1176 A 1 HETATM 48 C C4' RBF . B . C 2 -38.402 -1.311 31.038 0.44 41.55 ? C4' RBF 1176 A 1 HETATM 49 O O4' RBF . A . C 2 -37.676 -11.544 29.039 0.56 45.64 ? O4' RBF 1176 A 1 HETATM 50 O O4' RBF . B . C 2 -38.599 -2.712 31.264 0.44 41.36 ? O4' RBF 1176 A 1 HETATM 51 C C5' RBF . A . C 2 -36.634 -13.004 30.645 0.56 45.75 ? C5' RBF 1176 A 1 HETATM 52 C C5' RBF . B . C 2 -39.699 -0.7 30.522 0.44 41.72 ? C5' RBF 1176 A 1 HETATM 53 O O5' RBF . A . C 2 -35.494 -13.843 30.864 0.56 46.03 ? O5' RBF 1176 A 1 HETATM 54 O O5' RBF . B . C 2 -39.569 0.725 30.477 0.44 41.8 ? O5' RBF 1176 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 54 #