data_5BWM # _model_server_result.job_id TEK7dHQlqddFDNQP3j32qw _model_server_result.datetime_utc '2024-11-28 11:55:16' _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 5bwm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5BWM # _exptl.entry_id 5BWM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 5BWM _cell.length_a 50.479 _cell.length_b 50.479 _cell.length_c 136.671 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BWM _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,G,H,I _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 3 _struct_asym.id C _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 metalc ? metalc1 A OG1 THR 19 A THR 19 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc2 A O THR 37 A THR 37 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc3 C O1B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc4 C O3B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc5 D MG MG . A MG 202 1_555 H O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc6 D MG MG . A MG 202 1_555 H O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 92 n n PB O2B GDP sing 93 n n PB O3B GDP sing 94 n n PB O3A GDP sing 95 n n O2B HOB2 GDP sing 96 n n O3B HOB3 GDP sing 97 n n O3A PA GDP sing 98 n n PA O1A GDP doub 99 n n PA O2A GDP sing 100 n n PA O5' GDP sing 101 n n O2A HOA2 GDP sing 102 n n O5' C5' GDP sing 103 n n C5' C4' GDP sing 104 n n C5' H5' GDP sing 105 n n C5' "H5''" GDP sing 106 n n C4' O4' GDP sing 107 n n C4' C3' GDP sing 108 n n C4' H4' GDP sing 109 n n O4' C1' GDP sing 110 n n C3' O3' GDP sing 111 n n C3' C2' GDP sing 112 n n C3' H3' GDP sing 113 n n O3' HO3' GDP sing 114 n n C2' O2' GDP sing 115 n n C2' C1' GDP sing 116 n n C2' H2' GDP sing 117 n n O2' HO2' GDP sing 118 n n C1' N9 GDP sing 119 n n C1' H1' GDP sing 120 n n N9 C8 GDP sing 121 n y N9 C4 GDP sing 122 n y C8 N7 GDP doub 123 n y C8 H8 GDP sing 124 n n N7 C5 GDP sing 125 n y C5 C6 GDP sing 126 n n C5 C4 GDP doub 127 n y C6 O6 GDP doub 128 n n C6 N1 GDP sing 129 n n N1 C2 GDP sing 130 n n N1 HN1 GDP sing 131 n n C2 N2 GDP sing 132 n n C2 N3 GDP doub 133 n n N2 HN21 GDP sing 134 n n N2 HN22 GDP sing 135 n n N3 C4 GDP sing 136 n n # _atom_sites.entry_id 5BWM _atom_sites.fract_transf_matrix[1][1] 0.01981 _atom_sites.fract_transf_matrix[1][2] 0.011437 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022875 _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] 0.007317 _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 3 GDP A 1 201 200 GDP GDP . D 4 MG A 1 202 1 MG MG . E 5 NAI B 1 301 1 NAI NAI . F 6 EDO B 1 302 1 EDO EDO . G 6 EDO B 1 303 3 EDO EDO . H 7 HOH A 1 301 343 HOH HOH . H 7 HOH A 2 302 443 HOH HOH . H 7 HOH A 3 303 511 HOH HOH . H 7 HOH A 4 304 456 HOH HOH . H 7 HOH A 5 305 406 HOH HOH . H 7 HOH A 6 306 239 HOH HOH . H 7 HOH A 7 307 382 HOH HOH . H 7 HOH A 8 308 347 HOH HOH . H 7 HOH A 9 309 134 HOH HOH . H 7 HOH A 10 310 428 HOH HOH . H 7 HOH A 11 311 358 HOH HOH . H 7 HOH A 12 312 348 HOH HOH . H 7 HOH A 13 313 158 HOH HOH . H 7 HOH A 14 314 384 HOH HOH . H 7 HOH A 15 315 344 HOH HOH . H 7 HOH A 16 316 513 HOH HOH . H 7 HOH A 17 317 345 HOH HOH . H 7 HOH A 18 318 354 HOH HOH . H 7 HOH A 19 319 424 HOH HOH . H 7 HOH A 20 320 342 HOH HOH . H 7 HOH A 21 321 515 HOH HOH . H 7 HOH A 22 322 362 HOH HOH . H 7 HOH A 23 323 504 HOH HOH . H 7 HOH A 24 324 371 HOH HOH . H 7 HOH A 25 325 223 HOH HOH . H 7 HOH A 26 326 372 HOH HOH . H 7 HOH A 27 327 131 HOH HOH . H 7 HOH A 28 328 505 HOH HOH . H 7 HOH A 29 329 373 HOH HOH . H 7 HOH A 30 330 356 HOH HOH . I 7 HOH B 1 401 489 HOH HOH . I 7 HOH B 2 402 512 HOH HOH . I 7 HOH B 3 403 508 HOH HOH . I 7 HOH B 4 404 357 HOH HOH . I 7 HOH B 5 405 351 HOH HOH . I 7 HOH B 6 406 487 HOH HOH . I 7 HOH B 7 407 516 HOH HOH . I 7 HOH B 8 408 402 HOH HOH . I 7 HOH B 9 409 100 HOH HOH . I 7 HOH B 10 410 419 HOH HOH . I 7 HOH B 11 411 492 HOH HOH . I 7 HOH B 12 412 473 HOH HOH . I 7 HOH B 13 413 393 HOH HOH . I 7 HOH B 14 414 509 HOH HOH . I 7 HOH B 15 415 506 HOH HOH . I 7 HOH B 16 416 436 HOH HOH . I 7 HOH B 17 417 319 HOH HOH . I 7 HOH B 18 418 510 HOH HOH . I 7 HOH B 19 419 411 HOH HOH . I 7 HOH B 20 420 427 HOH HOH . I 7 HOH B 21 421 162 HOH HOH . I 7 HOH B 22 422 503 HOH HOH . I 7 HOH B 23 423 507 HOH HOH . I 7 HOH B 24 424 378 HOH HOH . I 7 HOH B 25 425 185 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 PB GDP . . . C 3 -0.764 18.95 23.807 1 55.02 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 -0.025 19.2 22.582 1 44.11 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 -0.175 19.928 24.846 1 51.65 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 -2.261 18.906 23.612 1 49.15 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 -0.215 17.503 24.327 1 63.15 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 -0.976 16.096 24.187 1 57.37 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 -1.165 15.905 22.736 1 46.03 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 -2.159 16.104 25.101 1 59.81 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 0.109 15.089 24.835 1 64.29 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 1.502 15.122 24.443 1 61.9 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 2.127 13.769 24.635 1 58.07 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 2.32 13.465 26.028 1 52.03 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 1.297 12.663 24.058 1 59.34 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 2.145 11.77 23.359 1 67.84 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 0.751 11.873 25.217 1 58.97 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 0.896 10.498 24.923 1 71.61 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 1.64 12.242 26.366 1 55.19 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 0.886 12.468 27.609 1 55.46 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 -0.2 13.26 27.775 1 56.31 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 -0.597 13.259 29.075 1 52.38 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 0.241 12.433 29.747 1 53.61 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 0.413 11.974 31.139 1 53.04 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 -0.35 12.343 32.064 1 55.4 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 1.425 11.126 31.388 1 65.16 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 2.282 10.683 30.443 1 56.36 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 3.272 9.834 30.795 1 55.86 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 2.18 11.075 29.159 1 58.93 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 1.214 11.923 28.773 1 57.26 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #