data_5CIQ # _model_server_result.job_id K5V1ztEnqEmBMHOg-OQoTQ _model_server_result.datetime_utc '2024-10-18 15:32:38' _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 5ciq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5CIQ # _exptl.entry_id 5CIQ _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 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 5CIQ _cell.length_a 102.68 _cell.length_b 102.68 _cell.length_c 41.89 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CIQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 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 ? 2 C N N ? 2 E 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 metalc ? metalc1 A OG1 THR 24 A THR 24 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc2 C O1B GDP . A GDP 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc3 D MG MG . A MG 302 1_555 G O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc4 D MG MG . A MG 302 1_555 G O HOH . A HOH 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc5 D MG MG . A MG 302 1_555 G O HOH . A HOH 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc6 D MG MG . A MG 302 1_555 G O HOH . A HOH 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc7 B OG1 THR 24 B THR 24 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc8 E O2B GDP . B GDP 301 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc9 F MG MG . B MG 302 1_555 H O HOH . B HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc10 F MG MG . B MG 302 1_555 H O HOH . B HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc11 F MG MG . B MG 302 1_555 H O HOH . B HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc12 F MG MG . B MG 302 1_555 H O HOH . B HOH 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? # _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 5CIQ _atom_sites.fract_transf_matrix[1][1] 0.009739 _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] 0.009739 _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] 0.023872 _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 2 GDP A 1 301 301 GDP GDP . D 3 MG A 1 302 1 MG MG . E 2 GDP B 1 301 301 GDP GDP . F 3 MG B 1 302 1 MG MG . G 4 HOH A 1 401 30 HOH HOH . G 4 HOH A 2 402 64 HOH HOH . G 4 HOH A 3 403 69 HOH HOH . G 4 HOH A 4 404 61 HOH HOH . G 4 HOH A 5 405 156 HOH HOH . G 4 HOH A 6 406 68 HOH HOH . G 4 HOH A 7 407 101 HOH HOH . G 4 HOH A 8 408 38 HOH HOH . G 4 HOH A 9 409 42 HOH HOH . G 4 HOH A 10 410 142 HOH HOH . G 4 HOH A 11 411 88 HOH HOH . G 4 HOH A 12 412 23 HOH HOH . G 4 HOH A 13 413 157 HOH HOH . G 4 HOH A 14 414 111 HOH HOH . G 4 HOH A 15 415 96 HOH HOH . G 4 HOH A 16 416 63 HOH HOH . G 4 HOH A 17 417 58 HOH HOH . G 4 HOH A 18 418 90 HOH HOH . G 4 HOH A 19 419 80 HOH HOH . G 4 HOH A 20 420 43 HOH HOH . G 4 HOH A 21 421 104 HOH HOH . G 4 HOH A 22 422 9 HOH HOH . G 4 HOH A 23 423 56 HOH HOH . G 4 HOH A 24 424 152 HOH HOH . G 4 HOH A 25 425 150 HOH HOH . G 4 HOH A 26 426 154 HOH HOH . G 4 HOH A 27 427 105 HOH HOH . G 4 HOH A 28 428 8 HOH HOH . G 4 HOH A 29 429 13 HOH HOH . G 4 HOH A 30 430 28 HOH HOH . G 4 HOH A 31 431 151 HOH HOH . G 4 HOH A 32 432 25 HOH HOH . G 4 HOH A 33 433 137 HOH HOH . G 4 HOH A 34 434 136 HOH HOH . G 4 HOH A 35 435 45 HOH HOH . G 4 HOH A 36 436 62 HOH HOH . G 4 HOH A 37 437 46 HOH HOH . G 4 HOH A 38 438 31 HOH HOH . G 4 HOH A 39 439 91 HOH HOH . G 4 HOH A 40 440 7 HOH HOH . G 4 HOH A 41 441 120 HOH HOH . G 4 HOH A 42 442 15 HOH HOH . G 4 HOH A 43 443 76 HOH HOH . G 4 HOH A 44 444 37 HOH HOH . G 4 HOH A 45 445 65 HOH HOH . G 4 HOH A 46 446 60 HOH HOH . G 4 HOH A 47 447 100 HOH HOH . G 4 HOH A 48 448 53 HOH HOH . G 4 HOH A 49 449 129 HOH HOH . G 4 HOH A 50 450 83 HOH HOH . G 4 HOH A 51 451 59 HOH HOH . G 4 HOH A 52 452 36 HOH HOH . G 4 HOH A 53 453 2 HOH HOH . G 4 HOH A 54 454 113 HOH HOH . G 4 HOH A 55 455 103 HOH HOH . G 4 HOH A 56 456 117 HOH HOH . G 4 HOH A 57 457 127 HOH HOH . G 4 HOH A 58 458 24 HOH HOH . G 4 HOH A 59 459 67 HOH HOH . G 4 HOH A 60 460 5 HOH HOH . G 4 HOH A 61 461 19 HOH HOH . G 4 HOH A 62 462 4 HOH HOH . G 4 HOH A 63 463 145 HOH HOH . G 4 HOH A 64 464 85 HOH HOH . G 4 HOH A 65 465 26 HOH HOH . G 4 HOH A 66 466 97 HOH HOH . G 4 HOH A 67 467 98 HOH HOH . G 4 HOH A 68 468 128 HOH HOH . G 4 HOH A 69 469 158 HOH HOH . G 4 HOH A 70 470 131 HOH HOH . G 4 HOH A 71 471 149 HOH HOH . G 4 HOH A 72 472 126 HOH HOH . G 4 HOH A 73 473 124 HOH HOH . G 4 HOH A 74 474 143 HOH HOH . G 4 HOH A 75 475 121 HOH HOH . G 4 HOH A 76 476 48 HOH HOH . G 4 HOH A 77 477 81 HOH HOH . G 4 HOH A 78 478 125 HOH HOH . H 4 HOH B 1 401 134 HOH HOH . H 4 HOH B 2 402 95 HOH HOH . H 4 HOH B 3 403 49 HOH HOH . H 4 HOH B 4 404 74 HOH HOH . H 4 HOH B 5 405 140 HOH HOH . H 4 HOH B 6 406 70 HOH HOH . H 4 HOH B 7 407 160 HOH HOH . H 4 HOH B 8 408 75 HOH HOH . H 4 HOH B 9 409 161 HOH HOH . H 4 HOH B 10 410 73 HOH HOH . H 4 HOH B 11 411 78 HOH HOH . H 4 HOH B 12 412 55 HOH HOH . H 4 HOH B 13 413 17 HOH HOH . H 4 HOH B 14 414 119 HOH HOH . H 4 HOH B 15 415 135 HOH HOH . H 4 HOH B 16 416 153 HOH HOH . H 4 HOH B 17 417 99 HOH HOH . H 4 HOH B 18 418 139 HOH HOH . H 4 HOH B 19 419 71 HOH HOH . H 4 HOH B 20 420 33 HOH HOH . H 4 HOH B 21 421 11 HOH HOH . H 4 HOH B 22 422 72 HOH HOH . H 4 HOH B 23 423 122 HOH HOH . H 4 HOH B 24 424 10 HOH HOH . H 4 HOH B 25 425 118 HOH HOH . H 4 HOH B 26 426 39 HOH HOH . H 4 HOH B 27 427 52 HOH HOH . H 4 HOH B 28 428 87 HOH HOH . H 4 HOH B 29 429 34 HOH HOH . H 4 HOH B 30 430 40 HOH HOH . H 4 HOH B 31 431 147 HOH HOH . H 4 HOH B 32 432 110 HOH HOH . H 4 HOH B 33 433 112 HOH HOH . H 4 HOH B 34 434 6 HOH HOH . H 4 HOH B 35 435 84 HOH HOH . H 4 HOH B 36 436 93 HOH HOH . H 4 HOH B 37 437 47 HOH HOH . H 4 HOH B 38 438 22 HOH HOH . H 4 HOH B 39 439 107 HOH HOH . H 4 HOH B 40 440 141 HOH HOH . H 4 HOH B 41 441 77 HOH HOH . H 4 HOH B 42 442 14 HOH HOH . H 4 HOH B 43 443 32 HOH HOH . H 4 HOH B 44 444 94 HOH HOH . H 4 HOH B 45 445 21 HOH HOH . H 4 HOH B 46 446 130 HOH HOH . H 4 HOH B 47 447 51 HOH HOH . H 4 HOH B 48 448 50 HOH HOH . H 4 HOH B 49 449 35 HOH HOH . H 4 HOH B 50 450 109 HOH HOH . H 4 HOH B 51 451 44 HOH HOH . H 4 HOH B 52 452 66 HOH HOH . H 4 HOH B 53 453 86 HOH HOH . H 4 HOH B 54 454 57 HOH HOH . H 4 HOH B 55 455 1 HOH HOH . H 4 HOH B 56 456 3 HOH HOH . H 4 HOH B 57 457 12 HOH HOH . H 4 HOH B 58 458 20 HOH HOH . H 4 HOH B 59 459 138 HOH HOH . H 4 HOH B 60 460 18 HOH HOH . H 4 HOH B 61 461 146 HOH HOH . H 4 HOH B 62 462 27 HOH HOH . H 4 HOH B 63 463 82 HOH HOH . H 4 HOH B 64 464 16 HOH HOH . H 4 HOH B 65 465 159 HOH HOH . H 4 HOH B 66 466 123 HOH HOH . H 4 HOH B 67 467 133 HOH HOH . H 4 HOH B 68 468 115 HOH HOH . H 4 HOH B 69 469 108 HOH HOH . H 4 HOH B 70 470 29 HOH HOH . H 4 HOH B 71 471 144 HOH HOH . H 4 HOH B 72 472 106 HOH HOH . H 4 HOH B 73 473 155 HOH HOH . H 4 HOH B 74 474 89 HOH HOH . H 4 HOH B 75 475 79 HOH HOH . H 4 HOH B 76 476 114 HOH HOH . H 4 HOH B 77 477 41 HOH HOH . H 4 HOH B 78 478 102 HOH HOH . H 4 HOH B 79 479 92 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 2 -19.192 45.839 8.206 1 16.63 ? PB GDP 301 A 1 HETATM 2 O O1B GDP . . . C 2 -18.124 45.885 7.208 1 15.24 ? O1B GDP 301 A 1 HETATM 3 O O2B GDP . . . C 2 -18.649 46.371 9.538 1 18.42 ? O2B GDP 301 A 1 HETATM 4 O O3B GDP . . . C 2 -20.452 46.527 7.704 1 17.85 ? O3B GDP 301 A 1 HETATM 5 O O3A GDP . . . C 2 -19.632 44.323 8.507 1 16.29 ? O3A GDP 301 A 1 HETATM 6 P PA GDP . . . C 2 -18.795 42.973 8.32 1 17.16 ? PA GDP 301 A 1 HETATM 7 O O1A GDP . . . C 2 -18.617 42.547 6.884 1 17.91 ? O1A GDP 301 A 1 HETATM 8 O O2A GDP . . . C 2 -17.475 43.079 9.1 1 18.95 ? O2A GDP 301 A 1 HETATM 9 O O5' GDP . . . C 2 -19.721 41.89 9.054 1 18.73 ? O5' GDP 301 A 1 HETATM 10 C C5' GDP . . . C 2 -20.137 42.131 10.437 1 20.03 ? C5' GDP 301 A 1 HETATM 11 C C4' GDP . . . C 2 -20.532 40.794 11.032 1 21.77 ? C4' GDP 301 A 1 HETATM 12 O O4' GDP . . . C 2 -21.759 40.327 10.382 1 21.4 ? O4' GDP 301 A 1 HETATM 13 C C3' GDP . . . C 2 -19.504 39.672 10.827 1 25.11 ? C3' GDP 301 A 1 HETATM 14 O O3' GDP . . . C 2 -19.692 38.791 11.937 1 25.23 ? O3' GDP 301 A 1 HETATM 15 C C2' GDP . . . C 2 -20.08 38.892 9.66 1 23.08 ? C2' GDP 301 A 1 HETATM 16 O O2' GDP . . . C 2 -19.722 37.497 9.511 1 26.22 ? O2' GDP 301 A 1 HETATM 17 C C1' GDP . . . C 2 -21.568 39.028 9.847 1 19.83 ? C1' GDP 301 A 1 HETATM 18 N N9 GDP . . . C 2 -22.276 38.985 8.545 1 18.96 ? N9 GDP 301 A 1 HETATM 19 C C8 GDP . . . C 2 -21.977 39.788 7.485 1 18.4 ? C8 GDP 301 A 1 HETATM 20 N N7 GDP . . . C 2 -22.907 39.505 6.512 1 19.55 ? N7 GDP 301 A 1 HETATM 21 C C5 GDP . . . C 2 -23.742 38.536 6.928 1 17.94 ? C5 GDP 301 A 1 HETATM 22 C C6 GDP . . . C 2 -24.855 37.776 6.365 1 20.02 ? C6 GDP 301 A 1 HETATM 23 O O6 GDP . . . C 2 -25.306 37.935 5.21 1 21.37 ? O6 GDP 301 A 1 HETATM 24 N N1 GDP . . . C 2 -25.427 36.865 7.151 1 19.59 ? N1 GDP 301 A 1 HETATM 25 C C2 GDP . . . C 2 -25.023 36.599 8.446 1 20.18 ? C2 GDP 301 A 1 HETATM 26 N N2 GDP . . . C 2 -25.681 35.705 9.145 1 23.95 ? N2 GDP 301 A 1 HETATM 27 N N3 GDP . . . C 2 -24.012 37.251 9.024 1 18.02 ? N3 GDP 301 A 1 HETATM 28 C C4 GDP . . . C 2 -23.345 38.2 8.295 1 18.8 ? C4 GDP 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #