data_4R3A # _model_server_result.job_id hEC9YFqOaCzcGy3xG2IPbQ _model_server_result.datetime_utc '2024-11-17 16:14:21' _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":"E","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 . . . E 4 16.386 25.364 53.972 1 38.66 ? N1 RBF 402 A 1 HETATM 2 C C2 RBF . . . E 4 16.33 25.202 52.628 1 51.67 ? C2 RBF 402 A 1 HETATM 3 O O2 RBF . . . E 4 17.323 25.371 51.954 1 74.6 ? O2 RBF 402 A 1 HETATM 4 N N3 RBF . . . E 4 15.179 24.859 52.026 1 29.23 ? N3 RBF 402 A 1 HETATM 5 C C4 RBF . . . E 4 14.05 24.69 52.745 1 26.88 ? C4 RBF 402 A 1 HETATM 6 O O4 RBF . . . E 4 13.006 24.392 52.182 1 12.61 ? O4 RBF 402 A 1 HETATM 7 C C4A RBF . . . E 4 14.065 24.881 54.126 1 30.8 ? C4A RBF 402 A 1 HETATM 8 N N5 RBF . . . E 4 12.942 24.754 54.847 1 24.52 ? N5 RBF 402 A 1 HETATM 9 C C5A RBF . . . E 4 12.959 24.948 56.165 1 13.06 ? C5A RBF 402 A 1 HETATM 10 C C6 RBF . . . E 4 11.753 24.795 56.891 1 16.98 ? C6 RBF 402 A 1 HETATM 11 C C7 RBF . . . E 4 11.732 24.991 58.261 1 17.61 ? C7 RBF 402 A 1 HETATM 12 C C7M RBF . . . E 4 10.394 24.812 58.996 1 31.08 ? C7M RBF 402 A 1 HETATM 13 C C8 RBF . . . E 4 12.88 25.336 58.94 1 32.41 ? C8 RBF 402 A 1 HETATM 14 C C8M RBF . . . E 4 12.887 25.558 60.453 1 32.65 ? C8M RBF 402 A 1 HETATM 15 C C9 RBF . . . E 4 14.08 25.494 58.241 1 24.31 ? C9 RBF 402 A 1 HETATM 16 C C9A RBF . . . E 4 14.138 25.299 56.839 1 19.74 ? C9A RBF 402 A 1 HETATM 17 N N10 RBF . . . E 4 15.326 25.447 56.135 1 24.45 ? N10 RBF 402 A 1 HETATM 18 C C10 RBF . . . E 4 15.286 25.237 54.745 1 35 ? C10 RBF 402 A 1 HETATM 19 C C1' RBF . . . E 4 16.591 25.821 56.773 1 32.53 ? C1' RBF 402 A 1 HETATM 20 C C2' RBF . . . E 4 17.373 24.58 57.222 1 31.67 ? C2' RBF 402 A 1 HETATM 21 O O2' RBF . . . E 4 16.502 23.564 57.583 1 35.66 ? O2' RBF 402 A 1 HETATM 22 C C3' RBF . . . E 4 18.256 24.918 58.413 1 48.32 ? C3' RBF 402 A 1 HETATM 23 O O3' RBF . . . E 4 17.447 25.214 59.522 1 72.26 ? O3' RBF 402 A 1 HETATM 24 C C4' RBF . . . E 4 19.161 26.103 58.103 1 47.44 ? C4' RBF 402 A 1 HETATM 25 O O4' RBF . . . E 4 19.679 25.964 56.807 1 33.25 ? O4' RBF 402 A 1 HETATM 26 C C5' RBF . . . E 4 20.298 26.158 59.115 1 62.85 ? C5' RBF 402 A 1 HETATM 27 O O5' RBF . . . E 4 21.338 25.278 58.758 1 53.41 ? O5' RBF 402 A 1 HETATM 28 H HN3 RBF . . . E 4 15.159 24.744 51.109 1 35.08 ? HN3 RBF 402 A 1 HETATM 29 H HC6 RBF . . . E 4 10.93 24.55 56.422 1 20.38 ? HC6 RBF 402 A 1 HETATM 30 H HC71 RBF . . . E 4 9.706 24.551 58.352 1 37.29 ? HC71 RBF 402 A 1 HETATM 31 H HC72 RBF . . . E 4 10.483 24.108 59.676 1 37.29 ? HC72 RBF 402 A 1 HETATM 32 H HC73 RBF . . . E 4 10.134 25.659 59.42 1 37.29 ? HC73 RBF 402 A 1 HETATM 33 H HC81 RBF . . . E 4 13.079 26.497 60.644 1 39.18 ? HC81 RBF 402 A 1 HETATM 34 H HC82 RBF . . . E 4 12.01 25.323 60.821 1 39.18 ? HC82 RBF 402 A 1 HETATM 35 H HC83 RBF . . . E 4 13.575 24.994 60.863 1 39.18 ? HC83 RBF 402 A 1 HETATM 36 H HC9 RBF . . . E 4 14.893 25.737 58.729 1 29.17 ? HC9 RBF 402 A 1 HETATM 37 H HC11 RBF . . . E 4 17.131 26.317 56.135 1 39.03 ? HC11 RBF 402 A 1 HETATM 38 H HC12 RBF . . . E 4 16.406 26.393 57.552 1 39.03 ? HC12 RBF 402 A 1 HETATM 39 H HC2' RBF . . . E 4 17.936 24.273 56.485 1 38 ? HC2' RBF 402 A 1 HETATM 40 H HO2' RBF . . . E 4 16.891 22.779 57.447 1 42.79 ? HO2' RBF 402 A 1 HETATM 41 H HC3' RBF . . . E 4 18.812 24.142 58.626 1 57.98 ? HC3' RBF 402 A 1 HETATM 42 H HO3' RBF . . . E 4 17.744 24.769 60.232 1 86.71 ? HO3' RBF 402 A 1 HETATM 43 H HC4' RBF . . . E 4 18.644 26.924 58.155 1 56.93 ? HC4' RBF 402 A 1 HETATM 44 H HO4' RBF . . . E 4 19.725 26.762 56.419 1 39.9 ? HO4' RBF 402 A 1 HETATM 45 H HC51 RBF . . . E 4 20.649 27.074 59.154 1 75.42 ? HC51 RBF 402 A 1 HETATM 46 H HC52 RBF . . . E 4 19.954 25.908 59.997 1 75.42 ? HC52 RBF 402 A 1 HETATM 47 H HO5' RBF . . . E 4 22.06 25.451 59.26 1 64.09 ? HO5' RBF 402 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 47 #