data_7JFP # _model_server_result.job_id ToRPmK8QUL7MrMgDqQNUYQ _model_server_result.datetime_utc '2025-01-15 21:37:02' _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 7jfp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 7JFP # _exptl.entry_id 7JFP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 7JFP _cell.length_a 99.645 _cell.length_b 99.645 _cell.length_c 134.262 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JFP _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 4 _struct_asym.id D _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 covale ? covale1 B C ASN 331 B ASN 331 1_555 B N CME 332 B CME 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 B C CME 332 B CME 332 1_555 B N ALA 333 B ALA 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 B OD2 ASP 220 B ASP 220 1_555 G MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc2 D O1B GDP . B GDP 401 1_555 G MG MG . B MG 404 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.83 ? metalc ? metalc3 D O1B GDP . B GDP 401 1_555 G MG MG . B MG 404 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.855 ? metalc ? metalc4 D O2B GDP . B GDP 401 1_555 G MG MG . B MG 404 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc5 D O3B GDP . B GDP 401 1_555 G MG MG . B MG 404 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc6 D O3A GDP . B GDP 401 1_555 G MG MG . B MG 404 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc7 D O3A GDP . B GDP 401 1_555 G MG MG . B MG 404 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc8 D O2A GDP . B GDP 401 1_555 G MG MG . B MG 404 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.453 ? # _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 104 n n PB O2B GDP sing 105 n n PB O3B GDP sing 106 n n PB O3A GDP sing 107 n n O2B HOB2 GDP sing 108 n n O3B HOB3 GDP sing 109 n n O3A PA GDP sing 110 n n PA O1A GDP doub 111 n n PA O2A GDP sing 112 n n PA O5' GDP sing 113 n n O2A HOA2 GDP sing 114 n n O5' C5' GDP sing 115 n n C5' C4' GDP sing 116 n n C5' H5' GDP sing 117 n n C5' "H5''" GDP sing 118 n n C4' O4' GDP sing 119 n n C4' C3' GDP sing 120 n n C4' H4' GDP sing 121 n n O4' C1' GDP sing 122 n n C3' O3' GDP sing 123 n n C3' C2' GDP sing 124 n n C3' H3' GDP sing 125 n n O3' HO3' GDP sing 126 n n C2' O2' GDP sing 127 n n C2' C1' GDP sing 128 n n C2' H2' GDP sing 129 n n O2' HO2' GDP sing 130 n n C1' N9 GDP sing 131 n n C1' H1' GDP sing 132 n n N9 C8 GDP sing 133 n y N9 C4 GDP sing 134 n y C8 N7 GDP doub 135 n y C8 H8 GDP sing 136 n n N7 C5 GDP sing 137 n y C5 C6 GDP sing 138 n n C5 C4 GDP doub 139 n y C6 O6 GDP doub 140 n n C6 N1 GDP sing 141 n n N1 C2 GDP sing 142 n n N1 HN1 GDP sing 143 n n C2 N2 GDP sing 144 n n C2 N3 GDP doub 145 n n N2 HN21 GDP sing 146 n n N2 HN22 GDP sing 147 n n N3 C4 GDP sing 148 n n # _atom_sites.entry_id 7JFP _atom_sites.fract_transf_matrix[1][1] 0.010036 _atom_sites.fract_transf_matrix[1][2] 0.005794 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011588 _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] 0.007448 _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 GOL A 1 401 401 GOL GOL . D 4 GDP B 1 401 401 GDP GDP . E 3 GOL B 1 402 501 GOL GOL . F 3 GOL B 1 403 601 GOL GOL . G 5 MG B 1 404 1 MG MG . H 6 HOH A 1 501 6 HOH HOH . H 6 HOH A 2 502 3 HOH HOH . H 6 HOH A 3 503 4 HOH HOH . I 6 HOH B 1 501 5 HOH HOH . I 6 HOH B 2 502 1 HOH HOH . I 6 HOH B 3 503 2 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 . A . D 4 2.116 35.761 34.572 0.51 112.55 ? PB GDP 401 B 1 HETATM 2 P PB GDP . B . D 4 1.999 37.413 33.177 0.49 105.44 ? PB GDP 401 B 1 HETATM 3 O O1B GDP . A . D 4 2.031 35.143 33.215 0.51 108.37 ? O1B GDP 401 B 1 HETATM 4 O O1B GDP . B . D 4 3.173 37.874 32.38 0.49 103.15 ? O1B GDP 401 B 1 HETATM 5 O O2B GDP . A . D 4 1.803 37.264 34.566 0.51 113.16 ? O2B GDP 401 B 1 HETATM 6 O O2B GDP . B . D 4 0.879 38.455 33.262 0.49 105.96 ? O2B GDP 401 B 1 HETATM 7 O O3B GDP . A . D 4 1.224 35.075 35.605 0.51 115.74 ? O3B GDP 401 B 1 HETATM 8 O O3B GDP . B . D 4 1.413 36.09 32.685 0.49 106.49 ? O3B GDP 401 B 1 HETATM 9 O O3A GDP . A . D 4 3.594 35.657 35.179 0.51 113.6 ? O3A GDP 401 B 1 HETATM 10 O O3A GDP . B . D 4 2.409 37.128 34.698 0.49 113.58 ? O3A GDP 401 B 1 HETATM 11 P PA GDP . A . D 4 4.264 34.795 36.339 0.51 110.72 ? PA GDP 401 B 1 HETATM 12 P PA GDP . B . D 4 2.78 35.795 35.488 0.49 114.24 ? PA GDP 401 B 1 HETATM 13 O O1A GDP . A . D 4 3.292 33.892 36.976 0.51 113.74 ? O1A GDP 401 B 1 HETATM 14 O O1A GDP . B . D 4 1.557 35.085 35.915 0.49 107.07 ? O1A GDP 401 B 1 HETATM 15 O O2A GDP . A . D 4 5.467 34.089 35.741 0.51 111.42 ? O2A GDP 401 B 1 HETATM 16 O O2A GDP . B . D 4 3.677 34.974 34.57 0.49 112.09 ? O2A GDP 401 B 1 HETATM 17 O O5' GDP . A . D 4 4.852 35.84 37.386 0.51 120.49 ? O5' GDP 401 B 1 HETATM 18 O O5' GDP . B . D 4 3.711 36.205 36.734 0.49 118.29 ? O5' GDP 401 B 1 HETATM 19 C C5' GDP . A . D 4 4.246 37.106 37.71 0.51 123.85 ? C5' GDP 401 B 1 HETATM 20 C C5' GDP . B . D 4 4.965 36.914 36.631 0.49 120.28 ? C5' GDP 401 B 1 HETATM 21 C C4' GDP . A . D 4 5.235 37.947 38.478 0.51 126.68 ? C4' GDP 401 B 1 HETATM 22 C C4' GDP . B . D 4 5.197 37.707 37.895 0.49 126.73 ? C4' GDP 401 B 1 HETATM 23 O O4' GDP . A . D 4 5.651 37.248 39.668 0.51 126.41 ? O4' GDP 401 B 1 HETATM 24 O O4' GDP . B . D 4 5.612 36.823 38.962 0.49 125.99 ? O4' GDP 401 B 1 HETATM 25 C C3' GDP . A . D 4 6.538 38.253 37.756 0.51 105.6 ? C3' GDP 401 B 1 HETATM 26 C C3' GDP . B . D 4 6.266 38.799 37.796 0.49 118.58 ? C3' GDP 401 B 1 HETATM 27 O O3' GDP . A . D 4 6.385 39.356 36.869 0.51 118.61 ? O3' GDP 401 B 1 HETATM 28 O O3' GDP . B . D 4 5.861 39.985 38.473 0.49 120.86 ? O3' GDP 401 B 1 HETATM 29 C C2' GDP . A . D 4 7.478 38.593 38.916 0.51 122.92 ? C2' GDP 401 B 1 HETATM 30 C C2' GDP . B . D 4 7.477 38.164 38.485 0.49 122.57 ? C2' GDP 401 B 1 HETATM 31 O O2' GDP . A . D 4 7.362 39.965 39.283 0.51 125.27 ? O2' GDP 401 B 1 HETATM 32 O O2' GDP . B . D 4 8.313 39.155 39.072 0.49 123.29 ? O2' GDP 401 B 1 HETATM 33 C C1' GDP . A . D 4 6.948 37.685 40.04 0.51 125.36 ? C1' GDP 401 B 1 HETATM 34 C C1' GDP . B . D 4 6.788 37.33 39.561 0.49 124.43 ? C1' GDP 401 B 1 HETATM 35 N N9 GDP . A . D 4 7.789 36.5 40.286 0.51 127.42 ? N9 GDP 401 B 1 HETATM 36 N N9 GDP . B . D 4 7.602 36.198 40.034 0.49 129.52 ? N9 GDP 401 B 1 HETATM 37 C C8 GDP . A . D 4 7.56 35.212 39.888 0.51 123.8 ? C8 GDP 401 B 1 HETATM 38 C C8 GDP . B . D 4 7.403 34.866 39.801 0.49 129.75 ? C8 GDP 401 B 1 HETATM 39 N N7 GDP . A . D 4 8.505 34.386 40.266 0.51 124.89 ? N7 GDP 401 B 1 HETATM 40 N N7 GDP . B . D 4 8.323 34.11 40.351 0.49 139.96 ? N7 GDP 401 B 1 HETATM 41 C C5 GDP . A . D 4 9.411 35.182 40.958 0.51 126.88 ? C5 GDP 401 B 1 HETATM 42 C C5 GDP . B . D 4 9.175 35.002 40.989 0.49 133.18 ? C5 GDP 401 B 1 HETATM 43 C C6 GDP . A . D 4 10.61 34.901 41.605 0.51 132.33 ? C6 GDP 401 B 1 HETATM 44 C C6 GDP . B . D 4 10.326 34.826 41.751 0.49 128.92 ? C6 GDP 401 B 1 HETATM 45 O O6 GDP . A . D 4 11.083 33.766 41.637 0.51 135.84 ? O6 GDP 401 B 1 HETATM 46 O O6 GDP . B . D 4 10.801 33.711 41.966 0.49 127.36 ? O6 GDP 401 B 1 HETATM 47 N N1 GDP . A . D 4 11.292 35.899 42.181 0.51 134.92 ? N1 GDP 401 B 1 HETATM 48 N N1 GDP . B . D 4 10.959 35.9 42.238 0.49 117.08 ? N1 GDP 401 B 1 HETATM 49 C C2 GDP . A . D 4 10.734 37.162 42.143 0.51 105.56 ? C2 GDP 401 B 1 HETATM 50 C C2 GDP . B . D 4 10.402 37.139 41.993 0.49 135.96 ? C2 GDP 401 B 1 HETATM 51 N N2 GDP . A . D 4 11.448 38.13 42.726 0.51 114.11 ? N2 GDP 401 B 1 HETATM 52 N N2 GDP . B . D 4 11.064 38.183 42.502 0.49 124.53 ? N2 GDP 401 B 1 HETATM 53 N N3 GDP . A . D 4 9.592 37.488 41.543 0.51 121.7 ? N3 GDP 401 B 1 HETATM 54 N N3 GDP . B . D 4 9.307 37.369 41.271 0.49 131.2 ? N3 GDP 401 B 1 HETATM 55 C C4 GDP . A . D 4 8.976 36.468 40.97 0.51 123.51 ? C4 GDP 401 B 1 HETATM 56 C C4 GDP . B . D 4 8.739 36.273 40.799 0.49 125.92 ? C4 GDP 401 B 1 HETATM 57 H HOB2 GDP . A . D 4 1.616 37.736 33.713 0.51 137.26 ? HOB2 GDP 401 B 1 HETATM 58 H HOB2 GDP . B . D 4 1.033 39.386 32.954 0.49 128.62 ? HOB2 GDP 401 B 1 HETATM 59 H HOB3 GDP . A . D 4 0.435 34.498 35.431 0.51 140.35 ? HOB3 GDP 401 B 1 HETATM 60 H HOB3 GDP . B . D 4 1.364 35.232 33.182 0.49 129.25 ? HOB3 GDP 401 B 1 HETATM 61 H HOA2 GDP . A . D 4 6.251 33.671 36.184 0.51 135.18 ? HOA2 GDP 401 B 1 HETATM 62 H HOA2 GDP . B . D 4 4.66 35.012 34.433 0.49 135.98 ? HOA2 GDP 401 B 1 HETATM 63 H H5' GDP . A . D 4 3.948 37.567 36.769 0.51 150.08 ? H5' GDP 401 B 1 HETATM 64 H H5' GDP . B . D 4 5.739 36.167 36.459 0.49 145.8 ? H5' GDP 401 B 1 HETATM 65 H "H5''" GDP . A . D 4 3.347 36.891 38.285 0.51 150.08 ? "H5''" GDP 401 B 1 HETATM 66 H "H5''" GDP . B . D 4 4.9 37.548 35.748 0.49 145.8 ? "H5''" GDP 401 B 1 HETATM 67 H H4' GDP . A . D 4 4.752 38.847 38.855 0.51 153.48 ? H4' GDP 401 B 1 HETATM 68 H H4' GDP . B . D 4 4.263 38.107 38.288 0.49 153.54 ? H4' GDP 401 B 1 HETATM 69 H H3' GDP . A . D 4 6.885 37.394 37.183 0.51 128.19 ? H3' GDP 401 B 1 HETATM 70 H H3' GDP . B . D 4 6.467 39.037 36.753 0.49 143.77 ? H3' GDP 401 B 1 HETATM 71 H HO3' GDP . A . D 4 6.163 40.148 37.426 0.51 143.8 ? HO3' GDP 401 B 1 HETATM 72 H HO3' GDP . B . D 4 6.107 40.75 37.889 0.49 146.5 ? HO3' GDP 401 B 1 HETATM 73 H H2' GDP . A . D 4 8.509 38.354 38.659 0.51 148.97 ? H2' GDP 401 B 1 HETATM 74 H H2' GDP . B . D 4 8.056 37.554 37.792 0.49 148.56 ? H2' GDP 401 B 1 HETATM 75 H HO2' GDP . A . D 4 8.269 40.362 39.213 0.51 151.79 ? HO2' GDP 401 B 1 HETATM 76 H HO2' GDP . B . D 4 9.184 39.12 38.596 0.49 149.42 ? HO2' GDP 401 B 1 HETATM 77 H H1' GDP . A . D 4 6.842 38.22 40.983 0.51 151.9 ? H1' GDP 401 B 1 HETATM 78 H H1' GDP . B . D 4 6.501 37.91 40.438 0.49 150.79 ? H1' GDP 401 B 1 HETATM 79 H H8 GDP . A . D 4 6.68 34.918 39.318 0.51 150.02 ? H8 GDP 401 B 1 HETATM 80 H H8 GDP . B . D 4 6.566 34.486 39.218 0.49 157.17 ? H8 GDP 401 B 1 HETATM 81 H HN1 GDP . A . D 4 12.3 35.804 42.108 0.51 163.37 ? HN1 GDP 401 B 1 HETATM 82 H HN1 GDP . B . D 4 11.97 35.81 42.254 0.49 141.97 ? HN1 GDP 401 B 1 HETATM 83 H HN21 GDP . A . D 4 11.151 39.1 42.767 0.51 138.4 ? HN21 GDP 401 B 1 HETATM 84 H HN21 GDP . B . D 4 11.922 38.097 43.037 0.49 150.91 ? HN21 GDP 401 B 1 HETATM 85 H HN22 GDP . A . D 4 12.346 37.975 43.174 0.51 138.4 ? HN22 GDP 401 B 1 HETATM 86 H HN22 GDP . B . D 4 10.762 39.146 42.395 0.49 150.91 ? HN22 GDP 401 B 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 86 #