data_7YCE # _model_server_result.job_id 6dIfgZx0h2WT-ttXxMxVBw _model_server_result.datetime_utc '2024-11-05 21:13:54' _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 7yce # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 7YCE # _exptl.entry_id 7YCE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 7YCE _cell.length_a 94.809 _cell.length_b 94.809 _cell.length_c 119.41 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YCE _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 2 _struct_asym.id B _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 OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc2 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 7YCE _atom_sites.fract_transf_matrix[1][1] 0.010548 _atom_sites.fract_transf_matrix[1][2] 0.00609 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012179 _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] 0.008375 _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 B 2 GDP A 1 201 201 GDP GDP . C 3 MG A 1 202 202 MG MG . D 4 SO4 A 1 203 203 SO4 SO4 . E 5 IQN A 1 204 301 IQN UNL . F 6 HOH A 1 301 99 HOH HOH . F 6 HOH A 2 302 29 HOH HOH . F 6 HOH A 3 303 66 HOH HOH . F 6 HOH A 4 304 24 HOH HOH . F 6 HOH A 5 305 18 HOH HOH . F 6 HOH A 6 306 22 HOH HOH . F 6 HOH A 7 307 61 HOH HOH . F 6 HOH A 8 308 97 HOH HOH . F 6 HOH A 9 309 47 HOH HOH . F 6 HOH A 10 310 49 HOH HOH . F 6 HOH A 11 311 3 HOH HOH . F 6 HOH A 12 312 35 HOH HOH . F 6 HOH A 13 313 6 HOH HOH . F 6 HOH A 14 314 52 HOH HOH . F 6 HOH A 15 315 76 HOH HOH . F 6 HOH A 16 316 40 HOH HOH . F 6 HOH A 17 317 25 HOH HOH . F 6 HOH A 18 318 82 HOH HOH . F 6 HOH A 19 319 28 HOH HOH . F 6 HOH A 20 320 14 HOH HOH . F 6 HOH A 21 321 60 HOH HOH . F 6 HOH A 22 322 36 HOH HOH . F 6 HOH A 23 323 75 HOH HOH . F 6 HOH A 24 324 93 HOH HOH . F 6 HOH A 25 325 92 HOH HOH . F 6 HOH A 26 326 27 HOH HOH . F 6 HOH A 27 327 5 HOH HOH . F 6 HOH A 28 328 34 HOH HOH . F 6 HOH A 29 329 4 HOH HOH . F 6 HOH A 30 330 2 HOH HOH . F 6 HOH A 31 331 1 HOH HOH . F 6 HOH A 32 332 13 HOH HOH . F 6 HOH A 33 333 58 HOH HOH . F 6 HOH A 34 334 12 HOH HOH . F 6 HOH A 35 335 31 HOH HOH . F 6 HOH A 36 336 41 HOH HOH . F 6 HOH A 37 337 96 HOH HOH . F 6 HOH A 38 338 10 HOH HOH . F 6 HOH A 39 339 7 HOH HOH . F 6 HOH A 40 340 78 HOH HOH . F 6 HOH A 41 341 51 HOH HOH . F 6 HOH A 42 342 68 HOH HOH . F 6 HOH A 43 343 30 HOH HOH . F 6 HOH A 44 344 59 HOH HOH . F 6 HOH A 45 345 15 HOH HOH . F 6 HOH A 46 346 16 HOH HOH . F 6 HOH A 47 347 8 HOH HOH . F 6 HOH A 48 348 83 HOH HOH . F 6 HOH A 49 349 32 HOH HOH . F 6 HOH A 50 350 23 HOH HOH . F 6 HOH A 51 351 64 HOH HOH . F 6 HOH A 52 352 69 HOH HOH . F 6 HOH A 53 353 77 HOH HOH . F 6 HOH A 54 354 85 HOH HOH . F 6 HOH A 55 355 19 HOH HOH . F 6 HOH A 56 356 79 HOH HOH . F 6 HOH A 57 357 70 HOH HOH . F 6 HOH A 58 358 95 HOH HOH . F 6 HOH A 59 359 56 HOH HOH . F 6 HOH A 60 360 20 HOH HOH . F 6 HOH A 61 361 74 HOH HOH . F 6 HOH A 62 362 71 HOH HOH . F 6 HOH A 63 363 62 HOH HOH . F 6 HOH A 64 364 38 HOH HOH . F 6 HOH A 65 365 45 HOH HOH . F 6 HOH A 66 366 87 HOH HOH . F 6 HOH A 67 367 11 HOH HOH . F 6 HOH A 68 368 46 HOH HOH . F 6 HOH A 69 369 73 HOH HOH . F 6 HOH A 70 370 86 HOH HOH . F 6 HOH A 71 371 63 HOH HOH . F 6 HOH A 72 372 55 HOH HOH . F 6 HOH A 73 373 94 HOH HOH . F 6 HOH A 74 374 48 HOH HOH . F 6 HOH A 75 375 88 HOH HOH . F 6 HOH A 76 376 42 HOH HOH . F 6 HOH A 77 377 21 HOH HOH . F 6 HOH A 78 378 65 HOH HOH . F 6 HOH A 79 379 39 HOH HOH . F 6 HOH A 80 380 53 HOH HOH . F 6 HOH A 81 381 9 HOH HOH . F 6 HOH A 82 382 37 HOH HOH . F 6 HOH A 83 383 90 HOH HOH . F 6 HOH A 84 384 26 HOH HOH . F 6 HOH A 85 385 50 HOH HOH . F 6 HOH A 86 386 98 HOH HOH . F 6 HOH A 87 387 44 HOH HOH . F 6 HOH A 88 388 91 HOH HOH . F 6 HOH A 89 389 89 HOH HOH . F 6 HOH A 90 390 84 HOH HOH . F 6 HOH A 91 391 67 HOH HOH . F 6 HOH A 92 392 54 HOH HOH . F 6 HOH A 93 393 80 HOH HOH . F 6 HOH A 94 394 43 HOH HOH . F 6 HOH A 95 395 72 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 . . . B 2 -7.886 14.204 -21.243 1 12.94 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -8.571 13.316 -22.299 1 13.81 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -8.805 15.27 -20.693 1 14.04 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -7.046 13.455 -20.256 1 13.12 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -6.821 15.047 -22.061 1 12.96 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -6.257 16.563 -21.978 1 14.91 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -7.254 17.473 -22.676 1 16.37 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -5.818 16.792 -20.516 1 15.75 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -4.968 16.655 -22.937 1 14.14 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -3.926 15.752 -22.57 1 15.58 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -2.656 16.302 -23.141 1 15.86 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -2.73 16.375 -24.567 1 15.61 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -2.417 17.724 -22.654 1 16.41 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -0.997 17.96 -22.645 1 18.33 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -3.058 18.52 -23.762 1 17.32 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -2.499 19.814 -23.823 1 20.87 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -2.634 17.727 -24.988 1 16.57 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -3.502 17.842 -26.139 1 16.15 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -4.869 17.749 -26.114 1 15.63 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -5.424 17.837 -27.292 1 15.08 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -4.363 18.007 -28.156 1 15.5 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -4.279 18.176 -29.606 1 14.91 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -5.185 18.227 -30.429 1 14.44 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -2.968 18.313 -30.007 1 16.34 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -1.838 18.262 -29.22 1 16.5 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -0.66 18.416 -29.904 1 15.87 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -1.931 18.118 -27.936 1 15.64 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -3.173 17.997 -27.455 1 15.7 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #