data_3CVY # _model_server_result.job_id Hjtlg8AnDyORgcPhLYa1FA _model_server_result.datetime_utc '2024-11-08 06:13:49' _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 3cvy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":521}' # _entry.id 3CVY # _exptl.entry_id 3CVY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 785.55 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FLAVIN-ADENINE DINUCLEOTIDE' _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 90 _cell.angle_gamma 90 _cell.entry_id 3CVY _cell.length_a 83.36 _cell.length_b 88.84 _cell.length_c 86.59 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CVY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 4 _struct_asym.id D _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 hydrog WATSON-CRICK hydrog1 A N3 DC 2 C DC 2 1_555 B N1 DG 15 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 2 C DC 2 1_555 B O6 DG 15 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 2 C DC 2 1_555 B N2 DG 15 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DA 3 C DA 3 1_555 B N3 DT 14 D DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 DA 3 C DA 3 1_555 B O4 DT 14 D DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DG 4 C DG 4 1_555 B N3 DC 13 D DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 DG 4 C DG 4 1_555 B O2 DC 13 D DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 DG 4 C DG 4 1_555 B N4 DC 13 D DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 DC 5 C DC 5 1_555 B N1 DG 12 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N4 DC 5 C DC 5 1_555 B O6 DG 12 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O2 DC 5 C DC 5 1_555 B N2 DG 12 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DG 6 C DG 6 1_555 B N3 DC 11 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 DG 6 C DG 6 1_555 B O2 DC 11 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 DG 6 C DG 6 1_555 B N4 DC 11 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 DG 7 C DG 7 1_555 B N3 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N2 DG 7 C DG 7 1_555 B O2 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O6 DG 7 C DG 7 1_555 B N4 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N1 DG 10 C DG 10 1_555 B N3 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N2 DG 10 C DG 10 1_555 B O2 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O6 DG 10 C DG 10 1_555 B N4 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 DC 11 C DC 11 1_555 B N1 DG 6 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 DC 11 C DC 11 1_555 B O6 DG 6 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 DC 11 C DC 11 1_555 B N2 DG 6 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog24 A N1 DA 12 C DA 12 1_555 B N3 DT 5 D DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 DG 13 C DG 13 1_555 B N3 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N2 DG 13 C DG 13 1_555 B O2 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O6 DG 13 C DG 13 1_555 B N4 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog28 A N1 DG 14 C DG 14 1_555 B N3 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DT MISPAIR' hydrog29 A N3 DT 15 C DT 15 1_555 B O4 DT 1 D DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 232 n n PA O2A FAD sing 233 n n PA O5B FAD sing 234 n n PA O3P FAD sing 235 n n O2A HOA2 FAD sing 236 n n O5B C5B FAD sing 237 n n C5B C4B FAD sing 238 n n C5B H51A FAD sing 239 n n C5B H52A FAD sing 240 n n C4B O4B FAD sing 241 n n C4B C3B FAD sing 242 n n C4B H4B FAD sing 243 n n O4B C1B FAD sing 244 n n C3B O3B FAD sing 245 n n C3B C2B FAD sing 246 n n C3B H3B FAD sing 247 n n O3B HO3A FAD sing 248 n n C2B O2B FAD sing 249 n n C2B C1B FAD sing 250 n n C2B H2B FAD sing 251 n n O2B HO2A FAD sing 252 n n C1B N9A FAD sing 253 n n C1B H1B FAD sing 254 n n N9A C8A FAD sing 255 n y N9A C4A FAD sing 256 n y C8A N7A FAD doub 257 n y C8A H8A FAD sing 258 n n N7A C5A FAD sing 259 n y C5A C6A FAD sing 260 n y C5A C4A FAD doub 261 n y C6A N6A FAD sing 262 n n C6A N1A FAD doub 263 n y N6A H61A FAD sing 264 n n N6A H62A FAD sing 265 n n N1A C2A FAD sing 266 n y C2A N3A FAD doub 267 n y C2A H2A FAD sing 268 n n N3A C4A FAD sing 269 n y N1 C2 FAD sing 270 n n N1 C10 FAD doub 271 n n C2 O2 FAD doub 272 n n C2 N3 FAD sing 273 n n N3 C4 FAD sing 274 n n N3 HN3 FAD sing 275 n n C4 O4 FAD doub 276 n n C4 C4X FAD sing 277 n n C4X N5 FAD doub 278 n n C4X C10 FAD sing 279 n n N5 C5X FAD sing 280 n n C5X C6 FAD doub 281 n y C5X C9A FAD sing 282 n y C6 C7 FAD sing 283 n y C6 H6 FAD sing 284 n n C7 C7M FAD sing 285 n n C7 C8 FAD doub 286 n y C7M HM71 FAD sing 287 n n C7M HM72 FAD sing 288 n n C7M HM73 FAD sing 289 n n C8 C8M FAD sing 290 n n C8 C9 FAD sing 291 n y C8M HM81 FAD sing 292 n n C8M HM82 FAD sing 293 n n C8M HM83 FAD sing 294 n n C9 C9A FAD doub 295 n y C9 H9 FAD sing 296 n n C9A N10 FAD sing 297 n n N10 C10 FAD sing 298 n n N10 C1' FAD sing 299 n n C1' C2' FAD sing 300 n n C1' "H1'1" FAD sing 301 n n C1' "H1'2" FAD sing 302 n n C2' O2' FAD sing 303 n n C2' C3' FAD sing 304 n n C2' H2' FAD sing 305 n n O2' HO2' FAD sing 306 n n C3' O3' FAD sing 307 n n C3' C4' FAD sing 308 n n C3' H3' FAD sing 309 n n O3' HO3' FAD sing 310 n n C4' O4' FAD sing 311 n n C4' C5' FAD sing 312 n n C4' H4' FAD sing 313 n n O4' HO4' FAD sing 314 n n C5' O5' FAD sing 315 n n C5' "H5'1" FAD sing 316 n n C5' "H5'2" FAD sing 317 n n O5' P FAD sing 318 n n P O1P FAD doub 319 n n P O2P FAD sing 320 n n P O3P FAD sing 321 n n O2P HOP2 FAD sing 322 n n # _atom_sites.entry_id 3CVY _atom_sites.fract_transf_matrix[1][1] 0.011996 _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] 0.011256 _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] 0.011549 _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 D 4 FAD A 1 521 1 FAD FAD . E 5 HOH C 1 16 5 HOH HOH . E 5 HOH C 2 17 6 HOH HOH . E 5 HOH C 3 18 11 HOH HOH . F 5 HOH A 1 522 3 HOH HOH . F 5 HOH A 2 523 8 HOH HOH . F 5 HOH A 3 524 9 HOH HOH . F 5 HOH A 4 525 10 HOH HOH . F 5 HOH A 5 526 12 HOH HOH . F 5 HOH A 6 527 13 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 P PA FAD . . . D 4 78.761 8.375 11.08 1 29.06 ? PA FAD 521 A 1 HETATM 2 O O1A FAD . . . D 4 77.967 8.028 12.317 1 28.57 ? O1A FAD 521 A 1 HETATM 3 O O2A FAD . . . D 4 79.383 9.746 11.202 1 27.56 ? O2A FAD 521 A 1 HETATM 4 O O5B FAD . . . D 4 77.828 8.285 9.77 1 28.17 ? O5B FAD 521 A 1 HETATM 5 C C5B FAD . . . D 4 76.824 7.304 9.683 1 28.75 ? C5B FAD 521 A 1 HETATM 6 C C4B FAD . . . D 4 77.091 6.328 8.545 1 28.94 ? C4B FAD 521 A 1 HETATM 7 O O4B FAD . . . D 4 77.162 6.997 7.299 1 29.09 ? O4B FAD 521 A 1 HETATM 8 C C3B FAD . . . D 4 78.399 5.56 8.67 1 29.31 ? C3B FAD 521 A 1 HETATM 9 O O3B FAD . . . D 4 78.322 4.437 9.521 1 29.02 ? O3B FAD 521 A 1 HETATM 10 C C2B FAD . . . D 4 78.67 5.202 7.225 1 29.28 ? C2B FAD 521 A 1 HETATM 11 O O2B FAD . . . D 4 77.971 4.042 6.845 1 28.9 ? O2B FAD 521 A 1 HETATM 12 C C1B FAD . . . D 4 78.159 6.419 6.475 1 29.23 ? C1B FAD 521 A 1 HETATM 13 N N9A FAD . . . D 4 79.295 7.338 6.268 1 29.34 ? N9A FAD 521 A 1 HETATM 14 C C8A FAD . . . D 4 79.798 8.268 7.146 1 29.7 ? C8A FAD 521 A 1 HETATM 15 N N7A FAD . . . D 4 80.844 8.898 6.563 1 29.78 ? N7A FAD 521 A 1 HETATM 16 C C5A FAD . . . D 4 81.018 8.386 5.329 1 29.54 ? C5A FAD 521 A 1 HETATM 17 C C6A FAD . . . D 4 81.932 8.666 4.324 1 29.65 ? C6A FAD 521 A 1 HETATM 18 N N6A FAD . . . D 4 82.741 9.721 4.426 1 29.42 ? N6A FAD 521 A 1 HETATM 19 N N1A FAD . . . D 4 81.863 7.96 3.14 1 29.65 ? N1A FAD 521 A 1 HETATM 20 C C2A FAD . . . D 4 80.899 6.99 2.959 1 29.62 ? C2A FAD 521 A 1 HETATM 21 N N3A FAD . . . D 4 79.994 6.718 3.966 1 29.69 ? N3A FAD 521 A 1 HETATM 22 C C4A FAD . . . D 4 80.053 7.406 5.132 1 29.69 ? C4A FAD 521 A 1 HETATM 23 N N1 FAD . . . D 4 83.633 3.81 5.814 1 26.51 ? N1 FAD 521 A 1 HETATM 24 C C2 FAD . . . D 4 83.208 2.506 5.67 1 26.66 ? C2 FAD 521 A 1 HETATM 25 O O2 FAD . . . D 4 82.075 2.189 6.024 1 26.89 ? O2 FAD 521 A 1 HETATM 26 N N3 FAD . . . D 4 84.047 1.556 5.127 1 26.56 ? N3 FAD 521 A 1 HETATM 27 C C4 FAD . . . D 4 85.315 1.929 4.734 1 26.47 ? C4 FAD 521 A 1 HETATM 28 O O4 FAD . . . D 4 86.112 1.05 4.443 1 27.03 ? O4 FAD 521 A 1 HETATM 29 C C4X FAD . . . D 4 85.749 3.242 4.878 1 26.29 ? C4X FAD 521 A 1 HETATM 30 N N5 FAD . . . D 4 87.016 3.606 4.484 1 27.06 ? N5 FAD 521 A 1 HETATM 31 C C5X FAD . . . D 4 87.45 4.917 4.627 1 26.86 ? C5X FAD 521 A 1 HETATM 32 C C6 FAD . . . D 4 88.739 5.267 4.221 1 26.44 ? C6 FAD 521 A 1 HETATM 33 C C7 FAD . . . D 4 89.192 6.579 4.358 1 26.62 ? C7 FAD 521 A 1 HETATM 34 C C7M FAD . . . D 4 90.548 6.956 3.813 1 26.53 ? C7M FAD 521 A 1 HETATM 35 C C8 FAD . . . D 4 88.347 7.538 4.905 1 26.41 ? C8 FAD 521 A 1 HETATM 36 C C8M FAD . . . D 4 88.883 8.873 5.323 1 26.78 ? C8M FAD 521 A 1 HETATM 37 C C9 FAD . . . D 4 87.066 7.185 5.306 1 26.51 ? C9 FAD 521 A 1 HETATM 38 C C9A FAD . . . D 4 86.597 5.874 5.175 1 26.49 ? C9A FAD 521 A 1 HETATM 39 N N10 FAD . . . D 4 85.313 5.509 5.575 1 26.26 ? N10 FAD 521 A 1 HETATM 40 C C10 FAD . . . D 4 84.901 4.194 5.423 1 26.18 ? C10 FAD 521 A 1 HETATM 41 C C1' FAD . . . D 4 84.224 6.555 5.618 1 26.72 ? C1' FAD 521 A 1 HETATM 42 C C2' FAD . . . D 4 83.929 6.983 7.058 1 26.6 ? C2' FAD 521 A 1 HETATM 43 O O2' FAD . . . D 4 85.126 7.301 7.721 1 25.96 ? O2' FAD 521 A 1 HETATM 44 C C3' FAD . . . D 4 83.21 5.911 7.87 1 27.21 ? C3' FAD 521 A 1 HETATM 45 O O3' FAD . . . D 4 82.088 5.435 7.151 1 27.08 ? O3' FAD 521 A 1 HETATM 46 C C4' FAD . . . D 4 82.767 6.459 9.224 1 27.11 ? C4' FAD 521 A 1 HETATM 47 O O4' FAD . . . D 4 83.895 6.888 9.948 1 27.83 ? O4' FAD 521 A 1 HETATM 48 C C5' FAD . . . D 4 82.048 5.389 10.023 1 26.48 ? C5' FAD 521 A 1 HETATM 49 O O5' FAD . . . D 4 81.833 5.807 11.35 1 26.39 ? O5' FAD 521 A 1 HETATM 50 P P FAD . . . D 4 80.348 6.138 11.853 1 25.7 ? P FAD 521 A 1 HETATM 51 O O1P FAD . . . D 4 79.511 4.888 11.741 1 26.35 ? O1P FAD 521 A 1 HETATM 52 O O2P FAD . . . D 4 80.345 6.672 13.26 1 25.52 ? O2P FAD 521 A 1 HETATM 53 O O3P FAD . . . D 4 79.878 7.245 10.79 1 27.51 ? O3P FAD 521 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 53 #