data_5NQT # _model_server_result.job_id 0cafLknW25NRAHtZIkcVKA _model_server_result.datetime_utc '2024-11-22 23:43:37' _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 5nqt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 5NQT # _exptl.entry_id 5NQT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 96.82 _cell.angle_gamma 90 _cell.entry_id 5NQT _cell.length_a 74.04 _cell.length_b 91.43 _cell.length_c 83.61 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NQT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 6 _struct_asym.id F _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 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc3 E MG MG . A MG 502 1_555 G O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 E MG MG . A MG 502 1_555 G O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc5 E MG MG . A MG 502 1_555 G O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? # _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 5NQT _atom_sites.fract_transf_matrix[1][1] 0.013506 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001615 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010937 _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] 0.012046 _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 D 4 GTP A 1 501 1 GTP GTP . E 5 MG A 1 502 503 MG MG . F 6 GDP B 1 501 1 GDP GDP . G 7 HOH A 1 601 65 HOH HOH . G 7 HOH A 2 602 60 HOH HOH . G 7 HOH A 3 603 2 HOH HOH . G 7 HOH A 4 604 59 HOH HOH . G 7 HOH A 5 605 37 HOH HOH . G 7 HOH A 6 606 25 HOH HOH . G 7 HOH A 7 607 20 HOH HOH . G 7 HOH A 8 608 15 HOH HOH . G 7 HOH A 9 609 34 HOH HOH . G 7 HOH A 10 610 69 HOH HOH . G 7 HOH A 11 611 73 HOH HOH . G 7 HOH A 12 612 68 HOH HOH . G 7 HOH A 13 613 11 HOH HOH . G 7 HOH A 14 614 44 HOH HOH . G 7 HOH A 15 615 4 HOH HOH . G 7 HOH A 16 616 3 HOH HOH . G 7 HOH A 17 617 1 HOH HOH . H 7 HOH B 1 601 43 HOH HOH . H 7 HOH B 2 602 29 HOH HOH . H 7 HOH B 3 603 1 HOH HOH . H 7 HOH B 4 604 5 HOH HOH . H 7 HOH B 5 605 42 HOH HOH . H 7 HOH B 6 606 81 HOH HOH . H 7 HOH B 7 607 5 HOH HOH . H 7 HOH B 8 608 2 HOH HOH . I 7 HOH F 1 201 9 HOH HOH . I 7 HOH F 2 202 19 HOH HOH . I 7 HOH F 3 203 6 HOH HOH . I 7 HOH F 4 204 30 HOH HOH . I 7 HOH F 5 205 4 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 . . . F 6 78.499 11.316 51.413 1 65.87 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . F 6 79.326 12.092 50.35 1 63.32 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . F 6 79.033 9.929 51.662 1 62.09 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . F 6 78.21 12.185 52.597 1 64.79 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . F 6 77.08 11.02 50.772 1 63.79 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . F 6 76.896 10.219 49.417 1 66.66 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . F 6 78.224 10.048 48.773 1 64.31 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . F 6 76.224 8.894 49.755 1 67.3 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . F 6 75.933 11.185 48.611 1 69.72 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . F 6 74.544 10.907 48.392 1 68.77 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . F 6 74.358 11.078 46.91 1 70.11 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . F 6 75.323 10.255 46.21 1 67.54 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . F 6 72.988 10.652 46.395 1 66.43 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . F 6 72.637 11.486 45.302 1 68.66 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . F 6 73.238 9.209 45.967 1 63.86 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . F 6 72.333 8.783 44.964 1 63.56 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . F 6 74.64 9.329 45.382 1 65.3 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . F 6 75.376 8.058 45.388 1 67.39 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . F 6 75.764 7.348 46.498 1 68.31 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . F 6 76.443 6.261 46.219 1 67.12 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . F 6 76.52 6.256 44.837 1 68.03 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . F 6 77.199 5.377 43.932 1 69.85 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . F 6 77.86 4.376 44.209 1 70.13 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . F 6 77.037 5.761 42.615 1 70.78 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . F 6 76.28 6.819 42.184 1 72.04 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . F 6 76.185 6.99 40.862 1 74.32 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . F 6 75.649 7.657 43.011 1 66.7 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . F 6 75.837 7.345 44.308 1 67.17 ? C4 GDP 501 B 1 HETATM 29 H H5' GDP . . . F 6 73.92 11.569 48.99 1 68.69 ? H5' GDP 501 B 1 HETATM 30 H "H5''" GDP . . . F 6 74.352 9.886 48.715 1 67.32 ? "H5''" GDP 501 B 1 HETATM 31 H H4' GDP . . . F 6 74.608 12.097 46.617 1 70.45 ? H4' GDP 501 B 1 HETATM 32 H H3' GDP . . . F 6 72.222 10.72 47.164 1 65.93 ? H3' GDP 501 B 1 HETATM 33 H HO3' GDP . . . F 6 71.925 11.021 44.789 1 68.97 ? HO3' GDP 501 B 1 HETATM 34 H H2' GDP . . . F 6 73.228 8.538 46.824 1 63.57 ? H2' GDP 501 B 1 HETATM 35 H HO2' GDP . . . F 6 71.851 8.016 45.368 1 64.04 ? HO2' GDP 501 B 1 HETATM 36 H H1' GDP . . . F 6 74.642 9.729 44.369 1 64.47 ? H1' GDP 501 B 1 HETATM 37 H H8 GDP . . . F 6 75.535 7.663 47.514 1 68.44 ? H8 GDP 501 B 1 HETATM 38 H HN1 GDP . . . F 6 77.567 5.223 41.939 1 69.8 ? HN1 GDP 501 B 1 HETATM 39 H HN21 GDP . . . F 6 75.643 7.76 40.484 1 74.79 ? HN21 GDP 501 B 1 HETATM 40 H HN22 GDP . . . F 6 76.63 6.383 40.182 1 74.2 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 40 #