data_4YQF # _model_server_result.job_id 7zyd74qZD7OHaJggkhtSdA _model_server_result.datetime_utc '2024-11-04 20:09:05' _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 4yqf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 4YQF # _exptl.entry_id 4YQF _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 105.81 _cell.angle_gamma 90 _cell.entry_id 4YQF _cell.length_a 57.04 _cell.length_b 77.523 _cell.length_c 77.909 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YQF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 OG SER 37 B SER 37 1_555 D MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc2 A OG1 THR 64 B THR 64 1_555 D MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc3 C O1B GDP . B GDP 301 1_555 D MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc4 C O3B GDP . B GDP 301 1_555 D MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? metalc ? metalc5 D MG MG . B MG 302 1_555 G O HOH . B HOH 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc6 D MG MG . B MG 302 1_555 G O HOH . B HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc7 B OG SER 37 A SER 37 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc8 B OG1 THR 64 A THR 64 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc9 E O2B GDP . A GDP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc10 F MG MG . A MG 302 1_555 H O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc11 F MG MG . A MG 302 1_555 H O HOH . A HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc12 F MG MG . A MG 302 1_555 H O HOH . A HOH 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? # _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 4YQF _atom_sites.fract_transf_matrix[1][1] 0.017532 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004966 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012899 _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] 0.01334 _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 B 1 301 3851 GDP GDP . D 3 MG B 1 302 2 MG MG . E 2 GDP A 1 301 3850 GDP GDP . F 3 MG A 1 302 1 MG MG . G 4 HOH B 1 401 61 HOH HOH . G 4 HOH B 2 402 23 HOH HOH . G 4 HOH B 3 403 27 HOH HOH . G 4 HOH B 4 404 66 HOH HOH . G 4 HOH B 5 405 78 HOH HOH . G 4 HOH B 6 406 2 HOH HOH . G 4 HOH B 7 407 4 HOH HOH . G 4 HOH B 8 408 5 HOH HOH . G 4 HOH B 9 409 7 HOH HOH . G 4 HOH B 10 410 10 HOH HOH . G 4 HOH B 11 411 11 HOH HOH . G 4 HOH B 12 412 14 HOH HOH . G 4 HOH B 13 413 16 HOH HOH . G 4 HOH B 14 414 17 HOH HOH . G 4 HOH B 15 415 18 HOH HOH . G 4 HOH B 16 416 20 HOH HOH . G 4 HOH B 17 417 26 HOH HOH . G 4 HOH B 18 418 28 HOH HOH . G 4 HOH B 19 419 29 HOH HOH . G 4 HOH B 20 420 30 HOH HOH . G 4 HOH B 21 421 31 HOH HOH . G 4 HOH B 22 422 34 HOH HOH . G 4 HOH B 23 423 38 HOH HOH . G 4 HOH B 24 424 39 HOH HOH . G 4 HOH B 25 425 41 HOH HOH . G 4 HOH B 26 426 52 HOH HOH . G 4 HOH B 27 427 53 HOH HOH . G 4 HOH B 28 428 54 HOH HOH . G 4 HOH B 29 429 57 HOH HOH . G 4 HOH B 30 430 58 HOH HOH . G 4 HOH B 31 431 59 HOH HOH . G 4 HOH B 32 432 63 HOH HOH . G 4 HOH B 33 433 65 HOH HOH . G 4 HOH B 34 434 67 HOH HOH . G 4 HOH B 35 435 68 HOH HOH . G 4 HOH B 36 436 69 HOH HOH . G 4 HOH B 37 437 70 HOH HOH . G 4 HOH B 38 438 72 HOH HOH . G 4 HOH B 39 439 73 HOH HOH . G 4 HOH B 40 440 75 HOH HOH . G 4 HOH B 41 441 85 HOH HOH . G 4 HOH B 42 442 86 HOH HOH . H 4 HOH A 1 401 62 HOH HOH . H 4 HOH A 2 402 6 HOH HOH . H 4 HOH A 3 403 76 HOH HOH . H 4 HOH A 4 404 37 HOH HOH . H 4 HOH A 5 405 19 HOH HOH . H 4 HOH A 6 406 15 HOH HOH . H 4 HOH A 7 407 74 HOH HOH . H 4 HOH A 8 408 1 HOH HOH . H 4 HOH A 9 409 3 HOH HOH . H 4 HOH A 10 410 8 HOH HOH . H 4 HOH A 11 411 9 HOH HOH . H 4 HOH A 12 412 12 HOH HOH . H 4 HOH A 13 413 13 HOH HOH . H 4 HOH A 14 414 21 HOH HOH . H 4 HOH A 15 415 22 HOH HOH . H 4 HOH A 16 416 24 HOH HOH . H 4 HOH A 17 417 25 HOH HOH . H 4 HOH A 18 418 32 HOH HOH . H 4 HOH A 19 419 33 HOH HOH . H 4 HOH A 20 420 35 HOH HOH . H 4 HOH A 21 421 40 HOH HOH . H 4 HOH A 22 422 42 HOH HOH . H 4 HOH A 23 423 44 HOH HOH . H 4 HOH A 24 424 45 HOH HOH . H 4 HOH A 25 425 46 HOH HOH . H 4 HOH A 26 426 47 HOH HOH . H 4 HOH A 27 427 48 HOH HOH . H 4 HOH A 28 428 50 HOH HOH . H 4 HOH A 29 429 51 HOH HOH . H 4 HOH A 30 430 55 HOH HOH . H 4 HOH A 31 431 56 HOH HOH . H 4 HOH A 32 432 60 HOH HOH . H 4 HOH A 33 433 64 HOH HOH . H 4 HOH A 34 434 71 HOH HOH . H 4 HOH A 35 435 77 HOH HOH . H 4 HOH A 36 436 80 HOH HOH . H 4 HOH A 37 437 81 HOH HOH . H 4 HOH A 38 438 82 HOH HOH . H 4 HOH A 39 439 83 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 32.018 -19.663 -42.987 1 28.74 ? PB GDP 301 B 1 HETATM 2 O O1B GDP . . . C 2 31.334 -20.009 -44.29 1 28.74 ? O1B GDP 301 B 1 HETATM 3 O O2B GDP . . . C 2 32.237 -18.173 -42.889 1 28.74 ? O2B GDP 301 B 1 HETATM 4 O O3B GDP . . . C 2 33.351 -20.365 -42.896 1 28.74 ? O3B GDP 301 B 1 HETATM 5 O O3A GDP . . . C 2 31.06 -20.129 -41.786 1 28.74 ? O3A GDP 301 B 1 HETATM 6 P PA GDP . . . C 2 30.473 -21.626 -41.695 1 28.74 ? PA GDP 301 B 1 HETATM 7 O O1A GDP . . . C 2 29.256 -21.799 -42.569 1 28.74 ? O1A GDP 301 B 1 HETATM 8 O O2A GDP . . . C 2 31.534 -22.655 -42.007 1 28.74 ? O2A GDP 301 B 1 HETATM 9 O O5' GDP . . . C 2 30.026 -21.676 -40.154 1 28.74 ? O5' GDP 301 B 1 HETATM 10 C C5' GDP . . . C 2 31.002 -21.808 -39.126 1 28.74 ? C5' GDP 301 B 1 HETATM 11 C C4' GDP . . . C 2 30.263 -22.111 -37.832 1 28.74 ? C4' GDP 301 B 1 HETATM 12 O O4' GDP . . . C 2 29.219 -21.153 -37.627 1 28.74 ? O4' GDP 301 B 1 HETATM 13 C C3' GDP . . . C 2 29.611 -23.479 -37.916 1 28.74 ? C3' GDP 301 B 1 HETATM 14 O O3' GDP . . . C 2 29.954 -24.232 -36.747 1 28.74 ? O3' GDP 301 B 1 HETATM 15 C C2' GDP . . . C 2 28.122 -23.194 -37.96 1 28.74 ? C2' GDP 301 B 1 HETATM 16 O O2' GDP . . . C 2 27.366 -24.196 -37.269 1 28.74 ? O2' GDP 301 B 1 HETATM 17 C C1' GDP . . . C 2 28.005 -21.827 -37.3 1 28.74 ? C1' GDP 301 B 1 HETATM 18 N N9 GDP . . . C 2 26.852 -21.071 -37.838 1 28.74 ? N9 GDP 301 B 1 HETATM 19 C C8 GDP . . . C 2 26.437 -21.04 -39.12 1 28.74 ? C8 GDP 301 B 1 HETATM 20 N N7 GDP . . . C 2 25.353 -20.235 -39.262 1 28.74 ? N7 GDP 301 B 1 HETATM 21 C C5 GDP . . . C 2 25.071 -19.726 -38.047 1 28.74 ? C5 GDP 301 B 1 HETATM 22 C C6 GDP . . . C 2 24.061 -18.804 -37.482 1 28.74 ? C6 GDP 301 B 1 HETATM 23 O O6 GDP . . . C 2 23.181 -18.291 -38.204 1 28.74 ? O6 GDP 301 B 1 HETATM 24 N N1 GDP . . . C 2 24.117 -18.538 -36.173 1 28.74 ? N1 GDP 301 B 1 HETATM 25 C C2 GDP . . . C 2 25.05 -19.075 -35.366 1 28.74 ? C2 GDP 301 B 1 HETATM 26 N N2 GDP . . . C 2 25.033 -18.751 -34.05 1 28.74 ? N2 GDP 301 B 1 HETATM 27 N N3 GDP . . . C 2 26.006 -19.927 -35.815 1 28.74 ? N3 GDP 301 B 1 HETATM 28 C C4 GDP . . . C 2 26.064 -20.279 -37.117 1 28.74 ? C4 GDP 301 B 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #