data_3VRB # _model_server_result.job_id '_H-Hs38EOYFXAu0nrQXutw' _model_server_result.datetime_utc '2024-11-24 14:42:36' _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 3vrb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":702}' # _entry.id 3VRB # _exptl.entry_id 3VRB _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 3VRB _cell.length_a 124.306 _cell.length_b 131.649 _cell.length_c 222.519 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VRB _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.788 ? covale ? covale2 E NE2 HIS 79 E HIS 79 1_555 R C8M FAD . E FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.685 ? metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.735 ? metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 W FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc26 W FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? # _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 208 n n PA O2A FAD sing 209 n n PA O5B FAD sing 210 n n PA O3P FAD sing 211 n n O2A HOA2 FAD sing 212 n n O5B C5B FAD sing 213 n n C5B C4B FAD sing 214 n n C5B H51A FAD sing 215 n n C5B H52A FAD sing 216 n n C4B O4B FAD sing 217 n n C4B C3B FAD sing 218 n n C4B H4B FAD sing 219 n n O4B C1B FAD sing 220 n n C3B O3B FAD sing 221 n n C3B C2B FAD sing 222 n n C3B H3B FAD sing 223 n n O3B HO3A FAD sing 224 n n C2B O2B FAD sing 225 n n C2B C1B FAD sing 226 n n C2B H2B FAD sing 227 n n O2B HO2A FAD sing 228 n n C1B N9A FAD sing 229 n n C1B H1B FAD sing 230 n n N9A C8A FAD sing 231 n y N9A C4A FAD sing 232 n y C8A N7A FAD doub 233 n y C8A H8A FAD sing 234 n n N7A C5A FAD sing 235 n y C5A C6A FAD sing 236 n y C5A C4A FAD doub 237 n y C6A N6A FAD sing 238 n n C6A N1A FAD doub 239 n y N6A H61A FAD sing 240 n n N6A H62A FAD sing 241 n n N1A C2A FAD sing 242 n y C2A N3A FAD doub 243 n y C2A H2A FAD sing 244 n n N3A C4A FAD sing 245 n y N1 C2 FAD sing 246 n n N1 C10 FAD doub 247 n n C2 O2 FAD doub 248 n n C2 N3 FAD sing 249 n n N3 C4 FAD sing 250 n n N3 HN3 FAD sing 251 n n C4 O4 FAD doub 252 n n C4 C4X FAD sing 253 n n C4X N5 FAD doub 254 n n C4X C10 FAD sing 255 n n N5 C5X FAD sing 256 n n C5X C6 FAD doub 257 n y C5X C9A FAD sing 258 n y C6 C7 FAD sing 259 n y C6 H6 FAD sing 260 n n C7 C7M FAD sing 261 n n C7 C8 FAD doub 262 n y C7M HM71 FAD sing 263 n n C7M HM72 FAD sing 264 n n C7M HM73 FAD sing 265 n n C8 C8M FAD sing 266 n n C8 C9 FAD sing 267 n y C8M HM81 FAD sing 268 n n C8M HM82 FAD sing 269 n n C8M HM83 FAD sing 270 n n C9 C9A FAD doub 271 n y C9 H9 FAD sing 272 n n C9A N10 FAD sing 273 n n N10 C10 FAD sing 274 n n N10 C1' FAD sing 275 n n C1' C2' FAD sing 276 n n C1' "H1'1" FAD sing 277 n n C1' "H1'2" FAD sing 278 n n C2' O2' FAD sing 279 n n C2' C3' FAD sing 280 n n C2' H2' FAD sing 281 n n O2' HO2' FAD sing 282 n n C3' O3' FAD sing 283 n n C3' C4' FAD sing 284 n n C3' H3' FAD sing 285 n n O3' HO3' FAD sing 286 n n C4' O4' FAD sing 287 n n C4' C5' FAD sing 288 n n C4' H4' FAD sing 289 n n O4' HO4' FAD sing 290 n n C5' O5' FAD sing 291 n n C5' "H5'1" FAD sing 292 n n C5' "H5'2" FAD sing 293 n n O5' P FAD sing 294 n n P O1P FAD doub 295 n n P O2P FAD sing 296 n n P O3P FAD sing 297 n n O2P HOP2 FAD sing 298 n n # _atom_sites.entry_id 3VRB _atom_sites.fract_transf_matrix[1][1] 0.008045 _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] 0.007596 _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] 0.004494 _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 FUM A 1 701 300 FUM FMR . 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 FTN C 1 202 810 FTN FTN . P 12 EPH D 1 201 306 EPH EPH . Q 5 FUM E 1 701 300 FUM FMR . 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 11 FTN F 1 304 810 FTN FTN . W 10 HEM G 1 201 305 HEM HEM . 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 . . . R 6 41.711 8.188 18.189 1 57.63 ? PA FAD 702 E 1 HETATM 2 O O1A FAD . . . R 6 41.222 8.448 16.791 1 60.34 ? O1A FAD 702 E 1 HETATM 3 O O2A FAD . . . R 6 40.714 7.409 18.974 1 59.22 ? O2A FAD 702 E 1 HETATM 4 O O5B FAD . . . R 6 41.976 9.593 18.885 1 60.68 ? O5B FAD 702 E 1 HETATM 5 C C5B FAD . . . R 6 41.535 10.695 18.139 1 63.06 ? C5B FAD 702 E 1 HETATM 6 C C4B FAD . . . R 6 41.462 11.95 18.971 1 64.5 ? C4B FAD 702 E 1 HETATM 7 O O4B FAD . . . R 6 42.362 12.945 18.512 1 64.68 ? O4B FAD 702 E 1 HETATM 8 C C3B FAD . . . R 6 40.085 12.491 18.726 1 66.8 ? C3B FAD 702 E 1 HETATM 9 O O3B FAD . . . R 6 39.499 12.736 19.984 1 68.93 ? O3B FAD 702 E 1 HETATM 10 C C2B FAD . . . R 6 40.289 13.772 17.931 1 67.03 ? C2B FAD 702 E 1 HETATM 11 O O2B FAD . . . R 6 39.291 14.73 18.245 1 69.2 ? O2B FAD 702 E 1 HETATM 12 C C1B FAD . . . R 6 41.675 14.17 18.382 1 65.44 ? C1B FAD 702 E 1 HETATM 13 N N9A FAD . . . R 6 42.339 15.135 17.494 1 65.64 ? N9A FAD 702 E 1 HETATM 14 C C8A FAD . . . R 6 43.123 14.896 16.404 1 65.98 ? C8A FAD 702 E 1 HETATM 15 N N7A FAD . . . R 6 43.525 16.091 15.919 1 66.3 ? N7A FAD 702 E 1 HETATM 16 C C5A FAD . . . R 6 43.026 17.087 16.692 1 66.77 ? C5A FAD 702 E 1 HETATM 17 C C6A FAD . . . R 6 43.113 18.493 16.667 1 68.25 ? C6A FAD 702 E 1 HETATM 18 N N6A FAD . . . R 6 43.871 19.165 15.79 1 68.56 ? N6A FAD 702 E 1 HETATM 19 N N1A FAD . . . R 6 42.454 19.233 17.627 1 68.89 ? N1A FAD 702 E 1 HETATM 20 C C2A FAD . . . R 6 41.725 18.593 18.607 1 68.55 ? C2A FAD 702 E 1 HETATM 21 N N3A FAD . . . R 6 41.648 17.216 18.619 1 67.11 ? N3A FAD 702 E 1 HETATM 22 C C4A FAD . . . R 6 42.282 16.48 17.682 1 66.04 ? C4A FAD 702 E 1 HETATM 23 N N1 FAD . . . R 6 43.057 -1.852 17.633 1 59.45 ? N1 FAD 702 E 1 HETATM 24 C C2 FAD . . . R 6 42.852 -2.972 18.417 1 61.47 ? C2 FAD 702 E 1 HETATM 25 O O2 FAD . . . R 6 43.623 -3.273 19.338 1 62.9 ? O2 FAD 702 E 1 HETATM 26 N N3 FAD . . . R 6 41.761 -3.775 18.171 1 61.6 ? N3 FAD 702 E 1 HETATM 27 C C4 FAD . . . R 6 40.873 -3.496 17.148 1 61.44 ? C4 FAD 702 E 1 HETATM 28 O O4 FAD . . . R 6 39.9 -4.224 16.913 1 63.42 ? O4 FAD 702 E 1 HETATM 29 C C4X FAD . . . R 6 41.079 -2.386 16.364 1 60.03 ? C4X FAD 702 E 1 HETATM 30 N N5 FAD . . . R 6 40.191 -2.128 15.335 1 59.09 ? N5 FAD 702 E 1 HETATM 31 C C5X FAD . . . R 6 40.393 -1.017 14.556 1 58.41 ? C5X FAD 702 E 1 HETATM 32 C C6 FAD . . . R 6 39.493 -0.731 13.529 1 58.64 ? C6 FAD 702 E 1 HETATM 33 C C7 FAD . . . R 6 39.671 0.404 12.73 1 56.66 ? C7 FAD 702 E 1 HETATM 34 C C7M FAD . . . R 6 38.686 0.686 11.637 1 53.35 ? C7M FAD 702 E 1 HETATM 35 C C8 FAD . . . R 6 40.77 1.227 12.993 1 56.27 ? C8 FAD 702 E 1 HETATM 36 C C8M FAD . . . R 6 41.056 2.433 12.171 1 56.72 ? C8M FAD 702 E 1 HETATM 37 C C9 FAD . . . R 6 41.667 0.94 14.012 1 56.12 ? C9 FAD 702 E 1 HETATM 38 C C9A FAD . . . R 6 41.484 -0.181 14.804 1 57.57 ? C9A FAD 702 E 1 HETATM 39 N N10 FAD . . . R 6 42.374 -0.47 15.829 1 59.13 ? N10 FAD 702 E 1 HETATM 40 C C10 FAD . . . R 6 42.171 -1.569 16.62 1 59.03 ? C10 FAD 702 E 1 HETATM 41 C C1' FAD . . . R 6 43.535 0.422 16.142 1 60.74 ? C1' FAD 702 E 1 HETATM 42 C C2' FAD . . . R 6 42.99 1.347 17.226 1 62.04 ? C2' FAD 702 E 1 HETATM 43 O O2' FAD . . . R 6 41.621 1.444 16.973 1 65.71 ? O2' FAD 702 E 1 HETATM 44 C C3' FAD . . . R 6 43.466 2.778 17.166 1 62.77 ? C3' FAD 702 E 1 HETATM 45 O O3' FAD . . . R 6 44.841 2.663 17.042 1 67.1 ? O3' FAD 702 E 1 HETATM 46 C C4' FAD . . . R 6 43.112 3.558 18.437 1 62.57 ? C4' FAD 702 E 1 HETATM 47 O O4' FAD . . . R 6 41.949 4.303 18.19 1 65.1 ? O4' FAD 702 E 1 HETATM 48 C C5' FAD . . . R 6 44.129 4.6 18.874 1 61.19 ? C5' FAD 702 E 1 HETATM 49 O O5' FAD . . . R 6 43.466 5.518 19.708 1 60.52 ? O5' FAD 702 E 1 HETATM 50 P P FAD . . . R 6 43.79 7.065 19.544 1 60.12 ? P FAD 702 E 1 HETATM 51 O O1P FAD . . . R 6 43.291 7.916 20.714 1 58.66 ? O1P FAD 702 E 1 HETATM 52 O O2P FAD . . . R 6 45.287 7.165 19.341 1 61.14 ? O2P FAD 702 E 1 HETATM 53 O O3P FAD . . . R 6 43.067 7.399 18.163 1 58.08 ? O3P FAD 702 E 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 53 #