data_3VRA # _model_server_result.job_id IUd6PBFesdyDqCuiSPmXdQ _model_server_result.datetime_utc '2024-11-24 14:11:28' _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 3vra # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":702}' # _entry.id 3VRA # _exptl.entry_id 3VRA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 785.55 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FLAVIN-ADENINE DINUCLEOTIDE' _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 3VRA _cell.length_a 122.823 _cell.length_b 132.25 _cell.length_c 220.577 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VRA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,B,C,D,I,J,K,L,M,N,O,P 1 1 E,F,G,H,Q,R,S,T,U,V,W,X 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 ? 6 J N N ? 6 R 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 NE2 HIS 79 A HIS 79 1_555 J C8M FAD . A FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.666 ? covale ? covale2 E NE2 HIS 79 E HIS 79 1_555 R C8M FAD . E FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc6 B SG CYS 188 B CYS 188 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc7 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc8 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc9 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc10 B SG CYS 249 B CYS 249 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc11 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc12 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc13 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc14 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc15 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc16 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc17 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc18 F SG CYS 188 F CYS 188 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc19 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc20 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc21 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc22 F SG CYS 249 F CYS 249 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc23 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc24 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _chem_comp.formula 'C27 H33 N9 O15 P2' _chem_comp.formula_weight 785.55 _chem_comp.id FAD _chem_comp.mon_nstd_flag . _chem_comp.name 'FLAVIN-ADENINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PA O1A FAD doub 252 n n PA O2A FAD sing 253 n n PA O5B FAD sing 254 n n PA O3P FAD sing 255 n n O2A HOA2 FAD sing 256 n n O5B C5B FAD sing 257 n n C5B C4B FAD sing 258 n n C5B H51A FAD sing 259 n n C5B H52A FAD sing 260 n n C4B O4B FAD sing 261 n n C4B C3B FAD sing 262 n n C4B H4B FAD sing 263 n n O4B C1B FAD sing 264 n n C3B O3B FAD sing 265 n n C3B C2B FAD sing 266 n n C3B H3B FAD sing 267 n n O3B HO3A FAD sing 268 n n C2B O2B FAD sing 269 n n C2B C1B FAD sing 270 n n C2B H2B FAD sing 271 n n O2B HO2A FAD sing 272 n n C1B N9A FAD sing 273 n n C1B H1B FAD sing 274 n n N9A C8A FAD sing 275 n y N9A C4A FAD sing 276 n y C8A N7A FAD doub 277 n y C8A H8A FAD sing 278 n n N7A C5A FAD sing 279 n y C5A C6A FAD sing 280 n y C5A C4A FAD doub 281 n y C6A N6A FAD sing 282 n n C6A N1A FAD doub 283 n y N6A H61A FAD sing 284 n n N6A H62A FAD sing 285 n n N1A C2A FAD sing 286 n y C2A N3A FAD doub 287 n y C2A H2A FAD sing 288 n n N3A C4A FAD sing 289 n y N1 C2 FAD sing 290 n n N1 C10 FAD doub 291 n n C2 O2 FAD doub 292 n n C2 N3 FAD sing 293 n n N3 C4 FAD sing 294 n n N3 HN3 FAD sing 295 n n C4 O4 FAD doub 296 n n C4 C4X FAD sing 297 n n C4X N5 FAD doub 298 n n C4X C10 FAD sing 299 n n N5 C5X FAD sing 300 n n C5X C6 FAD doub 301 n y C5X C9A FAD sing 302 n y C6 C7 FAD sing 303 n y C6 H6 FAD sing 304 n n C7 C7M FAD sing 305 n n C7 C8 FAD doub 306 n y C7M HM71 FAD sing 307 n n C7M HM72 FAD sing 308 n n C7M HM73 FAD sing 309 n n C8 C8M FAD sing 310 n n C8 C9 FAD sing 311 n y C8M HM81 FAD sing 312 n n C8M HM82 FAD sing 313 n n C8M HM83 FAD sing 314 n n C9 C9A FAD doub 315 n y C9 H9 FAD sing 316 n n C9A N10 FAD sing 317 n n N10 C10 FAD sing 318 n n N10 C1' FAD sing 319 n n C1' C2' FAD sing 320 n n C1' "H1'1" FAD sing 321 n n C1' "H1'2" FAD sing 322 n n C2' O2' FAD sing 323 n n C2' C3' FAD sing 324 n n C2' H2' FAD sing 325 n n O2' HO2' FAD sing 326 n n C3' O3' FAD sing 327 n n C3' C4' FAD sing 328 n n C3' H3' FAD sing 329 n n O3' HO3' FAD sing 330 n n C4' O4' FAD sing 331 n n C4' C5' FAD sing 332 n n C4' H4' FAD sing 333 n n O4' HO4' FAD sing 334 n n C5' O5' FAD sing 335 n n C5' "H5'1" FAD sing 336 n n C5' "H5'2" FAD sing 337 n n O5' P FAD sing 338 n n P O1P FAD doub 339 n n P O2P FAD sing 340 n n P O3P FAD sing 341 n n O2P HOP2 FAD sing 342 n n # _atom_sites.entry_id 3VRA _atom_sites.fract_transf_matrix[1][1] 0.008142 _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] 0.007561 _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] 0.004534 _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 I 5 MLI A 1 701 300 MLI MLI . J 6 FAD A 1 702 301 FAD FAD . K 7 FES B 1 301 302 FES FES . L 8 SF4 B 1 302 303 SF4 FS4 . M 9 F3S B 1 303 304 F3S F3S . N 10 HEM C 1 201 305 HEM HEM . O 11 AT5 C 1 202 811 AT5 AT5 . P 12 EPH D 1 201 306 EPH EPH . Q 5 MLI E 1 701 300 MLI MLI . R 6 FAD E 1 702 301 FAD FAD . S 7 FES F 1 301 302 FES FES . T 8 SF4 F 1 302 303 SF4 FS4 . U 9 F3S F 1 303 304 F3S F3S . V 10 HEM G 1 201 305 HEM HEM . W 11 AT5 G 1 202 811 AT5 AT5 . X 12 EPH H 1 201 306 EPH EPH . # 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 P PA FAD . . . J 6 9.103 -17.944 -40.426 1 92.25 ? PA FAD 702 A 1 HETATM 2 O O1A FAD . . . J 6 9.175 -17.885 -38.914 1 92.6 ? O1A FAD 702 A 1 HETATM 3 O O2A FAD . . . J 6 8.26 -16.855 -41.038 1 92.66 ? O2A FAD 702 A 1 HETATM 4 O O5B FAD . . . J 6 8.508 -19.367 -40.893 1 93.42 ? O5B FAD 702 A 1 HETATM 5 C C5B FAD . . . J 6 9.335 -20.453 -41.248 1 94.61 ? C5B FAD 702 A 1 HETATM 6 C C4B FAD . . . J 6 8.867 -21.147 -42.528 1 95.08 ? C4B FAD 702 A 1 HETATM 7 O O4B FAD . . . J 6 9.6 -22.346 -42.727 1 96.29 ? O4B FAD 702 A 1 HETATM 8 C C3B FAD . . . J 6 7.414 -21.567 -42.482 1 94.74 ? C3B FAD 702 A 1 HETATM 9 O O3B FAD . . . J 6 6.904 -21.273 -43.756 1 93.09 ? O3B FAD 702 A 1 HETATM 10 C C2B FAD . . . J 6 7.445 -23.06 -42.225 1 95.1 ? C2B FAD 702 A 1 HETATM 11 O O2B FAD . . . J 6 6.416 -23.743 -42.888 1 96.08 ? O2B FAD 702 A 1 HETATM 12 C C1B FAD . . . J 6 8.765 -23.486 -42.822 1 95.34 ? C1B FAD 702 A 1 HETATM 13 N N9A FAD . . . J 6 9.311 -24.672 -42.123 1 95.19 ? N9A FAD 702 A 1 HETATM 14 C C8A FAD . . . J 6 9.91 -24.751 -40.895 1 95.47 ? C8A FAD 702 A 1 HETATM 15 N N7A FAD . . . J 6 10.259 -26.039 -40.654 1 95.02 ? N7A FAD 702 A 1 HETATM 16 C C5A FAD . . . J 6 9.886 -26.792 -41.706 1 94.82 ? C5A FAD 702 A 1 HETATM 17 C C6A FAD . . . J 6 9.984 -28.159 -41.991 1 94.95 ? C6A FAD 702 A 1 HETATM 18 N N6A FAD . . . J 6 10.118 -29.07 -41.036 1 94.91 ? N6A FAD 702 A 1 HETATM 19 N N1A FAD . . . J 6 9.484 -28.617 -43.183 1 95.65 ? N1A FAD 702 A 1 HETATM 20 C C2A FAD . . . J 6 8.897 -27.745 -44.086 1 96.26 ? C2A FAD 702 A 1 HETATM 21 N N3A FAD . . . J 6 8.809 -26.396 -43.8 1 95.38 ? N3A FAD 702 A 1 HETATM 22 C C4A FAD . . . J 6 9.293 -25.934 -42.629 1 94.91 ? C4A FAD 702 A 1 HETATM 23 N N1 FAD . . . J 6 10.614 -9.027 -36.591 1 73.19 ? N1 FAD 702 A 1 HETATM 24 C C2 FAD . . . J 6 10.633 -7.72 -36.996 1 73.9 ? C2 FAD 702 A 1 HETATM 25 O O2 FAD . . . J 6 11.546 -7.306 -37.708 1 75.33 ? O2 FAD 702 A 1 HETATM 26 N N3 FAD . . . J 6 9.624 -6.878 -36.601 1 73.59 ? N3 FAD 702 A 1 HETATM 27 C C4 FAD . . . J 6 8.601 -7.32 -35.803 1 73.03 ? C4 FAD 702 A 1 HETATM 28 O O4 FAD . . . J 6 7.75 -6.506 -35.488 1 73.77 ? O4 FAD 702 A 1 HETATM 29 C C4X FAD . . . J 6 8.561 -8.644 -35.379 1 73.23 ? C4X FAD 702 A 1 HETATM 30 N N5 FAD . . . J 6 7.552 -9.148 -34.55 1 72.94 ? N5 FAD 702 A 1 HETATM 31 C C5X FAD . . . J 6 7.584 -10.484 -34.188 1 72.53 ? C5X FAD 702 A 1 HETATM 32 C C6 FAD . . . J 6 6.595 -11.058 -33.401 1 72.8 ? C6 FAD 702 A 1 HETATM 33 C C7 FAD . . . J 6 6.675 -12.429 -33.068 1 73.39 ? C7 FAD 702 A 1 HETATM 34 C C7M FAD . . . J 6 5.6 -13.03 -32.186 1 73.22 ? C7M FAD 702 A 1 HETATM 35 C C8 FAD . . . J 6 7.759 -13.21 -33.544 1 72.49 ? C8 FAD 702 A 1 HETATM 36 C C8M FAD . . . J 6 7.985 -14.654 -33.225 1 69.77 ? C8M FAD 702 A 1 HETATM 37 C C9 FAD . . . J 6 8.728 -12.634 -34.332 1 71.71 ? C9 FAD 702 A 1 HETATM 38 C C9A FAD . . . J 6 8.626 -11.291 -34.643 1 72.61 ? C9A FAD 702 A 1 HETATM 39 N N10 FAD . . . J 6 9.61 -10.778 -35.417 1 73.96 ? N10 FAD 702 A 1 HETATM 40 C C10 FAD . . . J 6 9.592 -9.475 -35.799 1 73.34 ? C10 FAD 702 A 1 HETATM 41 C C1' FAD . . . J 6 10.695 -11.677 -35.866 1 79.16 ? C1' FAD 702 A 1 HETATM 42 C C2' FAD . . . J 6 10.309 -12.187 -37.242 1 84.73 ? C2' FAD 702 A 1 HETATM 43 O O2' FAD . . . J 6 8.914 -12.122 -37.445 1 85.31 ? O2' FAD 702 A 1 HETATM 44 C C3' FAD . . . J 6 10.724 -13.633 -37.451 1 88.45 ? C3' FAD 702 A 1 HETATM 45 O O3' FAD . . . J 6 11.8 -13.998 -36.599 1 89.08 ? O3' FAD 702 A 1 HETATM 46 C C4' FAD . . . J 6 11.07 -13.826 -38.932 1 90.26 ? C4' FAD 702 A 1 HETATM 47 O O4' FAD . . . J 6 10.278 -12.993 -39.767 1 91.48 ? O4' FAD 702 A 1 HETATM 48 C C5' FAD . . . J 6 10.794 -15.26 -39.33 1 90.25 ? C5' FAD 702 A 1 HETATM 49 O O5' FAD . . . J 6 10.47 -15.279 -40.692 1 89.46 ? O5' FAD 702 A 1 HETATM 50 P P FAD . . . J 6 11.205 -16.41 -41.524 1 90.58 ? P FAD 702 A 1 HETATM 51 O O1P FAD . . . J 6 10.825 -16.393 -42.982 1 92.35 ? O1P FAD 702 A 1 HETATM 52 O O2P FAD . . . J 6 12.695 -16.269 -41.325 1 89.71 ? O2P FAD 702 A 1 HETATM 53 O O3P FAD . . . J 6 10.616 -17.8 -40.957 1 92.23 ? O3P FAD 702 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 53 #