data_4Q21 # _model_server_result.job_id Xki6rPAztb7zMu_O-5_oZw _model_server_result.datetime_utc '2024-11-23 06:09:30' _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 4q21 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":274}' # _entry.id 4Q21 # _exptl.entry_id 4Q21 _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 90 _cell.entry_id 4Q21 _cell.length_a 96.3 _cell.length_b 96.3 _cell.length_c 41.37 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q21 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 OG SER 17 A SER 17 1_555 B MG MG . A MG 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 B MG MG . A MG 273 1_555 C O3B GDP . A GDP 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc3 B MG MG . A MG 273 1_555 D O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc4 B MG MG . A MG 273 1_555 D O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc5 B MG MG . A MG 273 1_555 D O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc6 B MG MG . A MG 273 1_555 D O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? # _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 4Q21 _atom_sites.fract_transf_matrix[1][1] 0.010384 _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] 0.010384 _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] 0.024172 _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 MG A 1 273 273 MG MG . C 3 GDP A 1 274 180 GDP GDP . D 4 HOH A 1 401 401 HOH HOH . D 4 HOH A 2 402 402 HOH HOH . D 4 HOH A 3 403 403 HOH HOH . D 4 HOH A 4 404 404 HOH HOH . D 4 HOH A 5 405 405 HOH HOH . D 4 HOH A 6 406 406 HOH HOH . D 4 HOH A 7 407 407 HOH HOH . D 4 HOH A 8 408 408 HOH HOH . D 4 HOH A 9 409 409 HOH HOH . D 4 HOH A 10 410 410 HOH HOH . D 4 HOH A 11 411 411 HOH HOH . D 4 HOH A 12 412 412 HOH HOH . D 4 HOH A 13 413 413 HOH HOH . D 4 HOH A 14 414 414 HOH HOH . D 4 HOH A 15 415 415 HOH HOH . D 4 HOH A 16 416 416 HOH HOH . D 4 HOH A 17 417 417 HOH HOH . D 4 HOH A 18 418 418 HOH HOH . D 4 HOH A 19 419 419 HOH HOH . D 4 HOH A 20 420 420 HOH HOH . D 4 HOH A 21 421 421 HOH HOH . D 4 HOH A 22 422 422 HOH HOH . D 4 HOH A 23 423 423 HOH HOH . D 4 HOH A 24 424 424 HOH HOH . D 4 HOH A 25 425 425 HOH HOH . D 4 HOH A 26 426 426 HOH HOH . D 4 HOH A 27 427 427 HOH HOH . D 4 HOH A 28 428 428 HOH HOH . D 4 HOH A 29 429 429 HOH HOH . D 4 HOH A 30 430 430 HOH HOH . D 4 HOH A 31 431 431 HOH HOH . D 4 HOH A 32 432 432 HOH HOH . D 4 HOH A 33 433 433 HOH HOH . D 4 HOH A 34 434 434 HOH HOH . D 4 HOH A 35 435 435 HOH HOH . D 4 HOH A 36 436 436 HOH HOH . D 4 HOH A 37 437 437 HOH HOH . D 4 HOH A 38 438 438 HOH HOH . D 4 HOH A 39 439 439 HOH HOH . D 4 HOH A 40 440 440 HOH HOH . D 4 HOH A 41 441 441 HOH HOH . D 4 HOH A 42 442 442 HOH HOH . D 4 HOH A 43 443 443 HOH HOH . D 4 HOH A 44 444 444 HOH HOH . D 4 HOH A 45 445 445 HOH HOH . D 4 HOH A 46 446 446 HOH HOH . D 4 HOH A 47 447 447 HOH HOH . D 4 HOH A 48 448 448 HOH HOH . D 4 HOH A 49 449 449 HOH HOH . D 4 HOH A 50 450 450 HOH HOH . D 4 HOH A 51 451 451 HOH HOH . D 4 HOH A 52 452 452 HOH HOH . D 4 HOH A 53 453 453 HOH HOH . D 4 HOH A 54 454 454 HOH HOH . D 4 HOH A 55 455 455 HOH HOH . D 4 HOH A 56 456 456 HOH HOH . D 4 HOH A 57 457 457 HOH HOH . D 4 HOH A 58 458 458 HOH HOH . D 4 HOH A 59 459 459 HOH HOH . D 4 HOH A 60 460 460 HOH HOH . D 4 HOH A 61 461 461 HOH HOH . D 4 HOH A 62 462 462 HOH HOH . D 4 HOH A 63 463 463 HOH HOH . D 4 HOH A 64 464 464 HOH HOH . D 4 HOH A 65 465 465 HOH HOH . D 4 HOH A 66 466 466 HOH HOH . D 4 HOH A 67 467 467 HOH HOH . D 4 HOH A 68 468 468 HOH HOH . D 4 HOH A 69 469 469 HOH HOH . D 4 HOH A 70 470 470 HOH HOH . D 4 HOH A 71 471 471 HOH HOH . D 4 HOH A 72 472 472 HOH HOH . D 4 HOH A 73 473 473 HOH HOH . D 4 HOH A 74 474 474 HOH HOH . D 4 HOH A 75 475 475 HOH HOH . D 4 HOH A 76 476 476 HOH HOH . D 4 HOH A 77 477 477 HOH HOH . D 4 HOH A 78 478 478 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 62.667 77.781 47.505 1 31.08 ? PB GDP 274 A 1 HETATM 2 O O1B GDP . . . C 3 61.587 77.413 46.626 1 30.69 ? O1B GDP 274 A 1 HETATM 3 O O2B GDP . . . C 3 63.294 79.098 47.336 1 24.13 ? O2B GDP 274 A 1 HETATM 4 O O3B GDP . . . C 3 63.804 76.731 47.41 1 29.87 ? O3B GDP 274 A 1 HETATM 5 O O3A GDP . . . C 3 62.281 77.644 49.012 1 29.39 ? O3A GDP 274 A 1 HETATM 6 P PA GDP . . . C 3 62.781 76.563 50.116 1 32.94 ? PA GDP 274 A 1 HETATM 7 O O1A GDP . . . C 3 64.2 76.858 50.463 1 38.15 ? O1A GDP 274 A 1 HETATM 8 O O2A GDP . . . C 3 62.459 75.187 49.671 1 39.73 ? O2A GDP 274 A 1 HETATM 9 O O5' GDP . . . C 3 61.927 76.929 51.222 1 37.11 ? O5' GDP 274 A 1 HETATM 10 C C5' GDP . . . C 3 61.69 78.29 51.572 1 37.93 ? C5' GDP 274 A 1 HETATM 11 C C4' GDP . . . C 3 61.26 78.393 53.002 1 36.58 ? C4' GDP 274 A 1 HETATM 12 O O4' GDP . . . C 3 59.989 77.748 53.185 1 40.35 ? O4' GDP 274 A 1 HETATM 13 C C3' GDP . . . C 3 62.181 77.747 54.015 1 36.25 ? C3' GDP 274 A 1 HETATM 14 O O3' GDP . . . C 3 62.291 78.499 55.179 1 38.09 ? O3' GDP 274 A 1 HETATM 15 C C2' GDP . . . C 3 61.548 76.42 54.295 1 39.4 ? C2' GDP 274 A 1 HETATM 16 O O2' GDP . . . C 3 61.846 76.085 55.643 1 43.75 ? O2' GDP 274 A 1 HETATM 17 C C1' GDP . . . C 3 60.078 76.792 54.224 1 40.06 ? C1' GDP 274 A 1 HETATM 18 N N9 GDP . . . C 3 59.258 75.63 53.844 1 39.43 ? N9 GDP 274 A 1 HETATM 19 C C8 GDP . . . C 3 59.255 75.041 52.612 1 38.59 ? C8 GDP 274 A 1 HETATM 20 N N7 GDP . . . C 3 58.334 74.158 52.46 1 38.35 ? N7 GDP 274 A 1 HETATM 21 C C5 GDP . . . C 3 57.55 74.278 53.59 1 35.85 ? C5 GDP 274 A 1 HETATM 22 C C6 GDP . . . C 3 56.499 73.638 53.877 1 37.59 ? C6 GDP 274 A 1 HETATM 23 O O6 GDP . . . C 3 56.005 72.734 53.233 1 39.03 ? O6 GDP 274 A 1 HETATM 24 N N1 GDP . . . C 3 55.907 74.049 55.053 1 38.56 ? N1 GDP 274 A 1 HETATM 25 C C2 GDP . . . C 3 56.436 74.939 55.901 1 36.65 ? C2 GDP 274 A 1 HETATM 26 N N2 GDP . . . C 3 55.747 75.129 57.025 1 34.76 ? N2 GDP 274 A 1 HETATM 27 N N3 GDP . . . C 3 57.574 75.569 55.662 1 37.24 ? N3 GDP 274 A 1 HETATM 28 C C4 GDP . . . C 3 58.11 75.138 54.493 1 37.6 ? C4 GDP 274 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #