data_4R3A # _model_server_result.job_id 7rzUcrSBUjq7bPK29qI5gA _model_server_result.datetime_utc '2024-11-17 16:37:09' _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 4r3a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":402}' # _entry.id 4R3A # _exptl.entry_id 4R3A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.364 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RIBOFLAVIN _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 120 _cell.entry_id 4R3A _cell.length_a 98.882 _cell.length_b 98.882 _cell.length_c 422.255 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4R3A _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E 1 1 B,F,G,H 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 ? 4 E N N ? 4 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 disulf ? disulf1 A SG CYS 84 A CYS 78 1_555 A SG CYS 117 A CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 B SG CYS 84 B CYS 78 1_555 B SG CYS 117 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A OD1 ASN 256 A ASN 250 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc2 C MG MG . A MG 400 1_555 D O2G ANP . A ANP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? metalc ? metalc3 C MG MG . A MG 400 1_555 D O1A ANP . A ANP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc4 C MG MG . A MG 400 1_555 D O2B ANP . A ANP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc5 B OD1 ASN 256 B ASN 250 1_555 F MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc6 F MG MG . B MG 400 1_555 G O2G ANP . B ANP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc7 F MG MG . B MG 400 1_555 G O1A ANP . B ANP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc8 F MG MG . B MG 400 1_555 G O2B ANP . B ANP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? # _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 325 n n N1 C10 RBF doub 326 n n C2 O2 RBF doub 327 n n C2 N3 RBF sing 328 n n N3 C4 RBF sing 329 n n N3 HN3 RBF sing 330 n n C4 O4 RBF doub 331 n n C4 C4A RBF sing 332 n n C4A N5 RBF doub 333 n n C4A C10 RBF sing 334 n n N5 C5A RBF sing 335 n n C5A C6 RBF doub 336 n y C5A C9A RBF sing 337 n y C6 C7 RBF sing 338 n y C6 HC6 RBF sing 339 n n C7 C7M RBF sing 340 n n C7 C8 RBF doub 341 n y C7M HC71 RBF sing 342 n n C7M HC72 RBF sing 343 n n C7M HC73 RBF sing 344 n n C8 C8M RBF sing 345 n n C8 C9 RBF sing 346 n y C8M HC81 RBF sing 347 n n C8M HC82 RBF sing 348 n n C8M HC83 RBF sing 349 n n C9 C9A RBF doub 350 n y C9 HC9 RBF sing 351 n n C9A N10 RBF sing 352 n n N10 C10 RBF sing 353 n n N10 C1' RBF sing 354 n n C1' C2' RBF sing 355 n n C1' HC11 RBF sing 356 n n C1' HC12 RBF sing 357 n n C2' O2' RBF sing 358 n n C2' C3' RBF sing 359 n n C2' HC2' RBF sing 360 n n O2' HO2' RBF sing 361 n n C3' O3' RBF sing 362 n n C3' C4' RBF sing 363 n n C3' HC3' RBF sing 364 n n O3' HO3' RBF sing 365 n n C4' O4' RBF sing 366 n n C4' C5' RBF sing 367 n n C4' HC4' RBF sing 368 n n O4' HO4' RBF sing 369 n n C5' O5' RBF sing 370 n n C5' HC51 RBF sing 371 n n C5' HC52 RBF sing 372 n n O5' HO5' RBF sing 373 n n # _atom_sites.entry_id 4R3A _atom_sites.fract_transf_matrix[1][1] 0.010113 _atom_sites.fract_transf_matrix[1][2] 0.005839 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011678 _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] 0.002368 _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 MG A 1 400 400 MG MG . D 3 ANP A 1 401 401 ANP ANP . E 4 RBF A 1 402 402 RBF RBF . F 2 MG B 1 400 400 MG MG . G 3 ANP B 1 401 401 ANP ANP . H 4 RBF B 1 402 402 RBF RBF . # 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 . . . H 4 10.191 28.112 13.155 1 132.52 ? N1 RBF 402 B 1 HETATM 2 C C2 RBF . . . H 4 10.593 28.256 14.441 1 142.01 ? C2 RBF 402 B 1 HETATM 3 O O2 RBF . . . H 4 11.747 28.03 14.736 1 133.28 ? O2 RBF 402 B 1 HETATM 4 N N3 RBF . . . H 4 9.726 28.646 15.391 1 138.03 ? N3 RBF 402 B 1 HETATM 5 C C4 RBF . . . H 4 8.449 28.931 15.071 1 143.96 ? C4 RBF 402 B 1 HETATM 6 O O4 RBF . . . H 4 7.671 29.288 15.94 1 158.73 ? O4 RBF 402 B 1 HETATM 7 C C4A RBF . . . H 4 8.007 28.818 13.751 1 138.94 ? C4A RBF 402 B 1 HETATM 8 N N5 RBF . . . H 4 6.74 29.105 13.41 1 183.57 ? N5 RBF 402 B 1 HETATM 9 C C5A RBF . . . H 4 6.328 28.997 12.148 1 140.6 ? C5A RBF 402 B 1 HETATM 10 C C6 RBF . . . H 4 4.982 29.312 11.828 1 161.52 ? C6 RBF 402 B 1 HETATM 11 C C7 RBF . . . H 4 4.502 29.212 10.526 1 172.31 ? C7 RBF 402 B 1 HETATM 12 C C7M RBF . . . H 4 3.019 29.582 10.306 1 190.58 ? C7M RBF 402 B 1 HETATM 13 C C8 RBF . . . H 4 5.355 28.798 9.515 1 159.83 ? C8 RBF 402 B 1 HETATM 14 C C8M RBF . . . H 4 4.934 28.654 8.056 1 172 ? C8M RBF 402 B 1 HETATM 15 C C9 RBF . . . H 4 6.684 28.484 9.813 1 197.26 ? C9 RBF 402 B 1 HETATM 16 C C9A RBF . . . H 4 7.192 28.58 11.134 1 131.69 ? C9A RBF 402 B 1 HETATM 17 N N10 RBF . . . H 4 8.51 28.272 11.434 1 137.92 ? N10 RBF 402 B 1 HETATM 18 C C10 RBF . . . H 4 8.925 28.39 12.771 1 133.34 ? C10 RBF 402 B 1 HETATM 19 C C1' RBF . . . H 4 9.478 27.814 10.438 1 130.72 ? C1' RBF 402 B 1 HETATM 20 C C2' RBF . . . H 4 10.337 28.966 9.904 1 128.92 ? C2' RBF 402 B 1 HETATM 21 O O2' RBF . . . H 4 9.524 30.039 9.571 1 121.46 ? O2' RBF 402 B 1 HETATM 22 C C3' RBF . . . H 4 11.114 28.518 8.671 1 121.97 ? C3' RBF 402 B 1 HETATM 23 O O3' RBF . . . H 4 10.21 28.197 7.648 1 123.73 ? O3' RBF 402 B 1 HETATM 24 C C4' RBF . . . H 4 11.99 27.307 8.977 1 131.78 ? C4' RBF 402 B 1 HETATM 25 O O4' RBF . . . H 4 12.892 27.628 10.003 1 123.75 ? O4' RBF 402 B 1 HETATM 26 C C5' RBF . . . H 4 12.769 26.889 7.74 1 127.59 ? C5' RBF 402 B 1 HETATM 27 O O5' RBF . . . H 4 13.764 27.84 7.452 1 133.15 ? O5' RBF 402 B 1 HETATM 28 H HN3 RBF . . . H 4 10.01 28.733 16.266 1 165.64 ? HN3 RBF 402 B 1 HETATM 29 H HC6 RBF . . . H 4 4.378 29.605 12.539 1 193.82 ? HC6 RBF 402 B 1 HETATM 30 H HC71 RBF . . . H 4 2.792 29.469 9.361 1 228.69 ? HC71 RBF 402 B 1 HETATM 31 H HC72 RBF . . . H 4 2.873 30.517 10.568 1 228.69 ? HC72 RBF 402 B 1 HETATM 32 H HC73 RBF . . . H 4 2.451 28.995 10.852 1 228.69 ? HC73 RBF 402 B 1 HETATM 33 H HC81 RBF . . . H 4 4.97 27.711 7.798 1 206.4 ? HC81 RBF 402 B 1 HETATM 34 H HC82 RBF . . . H 4 4.019 28.988 7.946 1 206.4 ? HC82 RBF 402 B 1 HETATM 35 H HC83 RBF . . . H 4 5.541 29.172 7.488 1 206.4 ? HC83 RBF 402 B 1 HETATM 36 H HC9 RBF . . . H 4 7.277 28.191 9.094 1 236.71 ? HC9 RBF 402 B 1 HETATM 37 H HC11 RBF . . . H 4 10.066 27.16 10.853 1 156.86 ? HC11 RBF 402 B 1 HETATM 38 H HC12 RBF . . . H 4 8.999 27.386 9.692 1 156.86 ? HC12 RBF 402 B 1 HETATM 39 H HC2' RBF . . . H 4 10.967 29.244 10.596 1 154.7 ? HC2' RBF 402 B 1 HETATM 40 H HO2' RBF . . . H 4 9.974 30.795 9.68 1 145.75 ? HO2' RBF 402 B 1 HETATM 41 H HC3' RBF . . . H 4 11.684 29.254 8.371 1 146.36 ? HC3' RBF 402 B 1 HETATM 42 H HO3' RBF . . . H 4 10.328 28.753 6.964 1 148.48 ? HO3' RBF 402 B 1 HETATM 43 H HC4' RBF . . . H 4 11.428 26.57 9.265 1 158.13 ? HC4' RBF 402 B 1 HETATM 44 H HO4' RBF . . . H 4 13.272 26.884 10.307 1 148.5 ? HO4' RBF 402 B 1 HETATM 45 H HC51 RBF . . . H 4 12.155 26.819 6.977 1 153.11 ? HC51 RBF 402 B 1 HETATM 46 H HC52 RBF . . . H 4 13.188 26.019 7.9 1 153.11 ? HC52 RBF 402 B 1 HETATM 47 H HO5' RBF . . . H 4 14.317 27.513 6.829 1 159.78 ? HO5' RBF 402 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 47 #