data_3NBY # _model_server_result.job_id s_BrGF-gntYCTbwno-YySg _model_server_result.datetime_utc '2024-11-23 10:27:47' _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 3nby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":217}' # _entry.id 3NBY # _exptl.entry_id 3NBY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 100.63 _cell.angle_gamma 90 _cell.entry_id 3NBY _cell.length_a 72.09 _cell.length_b 223.726 _cell.length_c 163.064 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NBY _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 PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H 1 1 D,E,F,I,J 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 ? 4 G N N ? 4 J 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 G O3G GTP . C GTP 217 1_555 H MG MG . C MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc2 G O2B GTP . C GTP 217 1_555 H MG MG . C MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc3 E OG1 THR 20 F THR 24 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc4 E OG1 THR 38 F THR 42 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc5 J O1B GTP . F GTP 217 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc6 J O1G GTP . F GTP 217 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc7 J O3G GTP . F GTP 217 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G GTP doub 129 n n PG O2G GTP sing 130 n n PG O3G GTP sing 131 n n PG O3B GTP sing 132 n n O2G HOG2 GTP sing 133 n n O3G HOG3 GTP sing 134 n n O3B PB GTP sing 135 n n PB O1B GTP doub 136 n n PB O2B GTP sing 137 n n PB O3A GTP sing 138 n n O2B HOB2 GTP sing 139 n n O3A PA GTP sing 140 n n PA O1A GTP doub 141 n n PA O2A GTP sing 142 n n PA O5' GTP sing 143 n n O2A HOA2 GTP sing 144 n n O5' C5' GTP sing 145 n n C5' C4' GTP sing 146 n n C5' H5' GTP sing 147 n n C5' "H5''" GTP sing 148 n n C4' O4' GTP sing 149 n n C4' C3' GTP sing 150 n n C4' H4' GTP sing 151 n n O4' C1' GTP sing 152 n n C3' O3' GTP sing 153 n n C3' C2' GTP sing 154 n n C3' H3' GTP sing 155 n n O3' HO3' GTP sing 156 n n C2' O2' GTP sing 157 n n C2' C1' GTP sing 158 n n C2' H2' GTP sing 159 n n O2' HO2' GTP sing 160 n n C1' N9 GTP sing 161 n n C1' H1' GTP sing 162 n n N9 C8 GTP sing 163 n y N9 C4 GTP sing 164 n y C8 N7 GTP doub 165 n y C8 H8 GTP sing 166 n n N7 C5 GTP sing 167 n y C5 C6 GTP sing 168 n n C5 C4 GTP doub 169 n y C6 O6 GTP doub 170 n n C6 N1 GTP sing 171 n n N1 C2 GTP sing 172 n n N1 HN1 GTP sing 173 n n C2 N2 GTP sing 174 n n C2 N3 GTP doub 175 n n N2 HN21 GTP sing 176 n n N2 HN22 GTP sing 177 n n N3 C4 GTP sing 178 n n # _atom_sites.entry_id 3NBY _atom_sites.fract_transf_matrix[1][1] 0.013872 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002604 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00447 _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] 0.00624 _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 G 4 GTP C 1 217 217 GTP GTP . H 5 MG C 1 218 218 MG MG . I 5 MG F 1 218 218 MG MG . J 4 GTP F 1 217 217 GTP GTP . # 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 PG GTP . . . J 4 0.248 -109.888 38.989 1 25.98 ? PG GTP 217 F 1 HETATM 2 O O1G GTP . . . J 4 -1.186 -110.316 38.793 1 29.24 ? O1G GTP 217 F 1 HETATM 3 O O2G GTP . . . J 4 0.378 -108.405 39.278 1 9.44 ? O2G GTP 217 F 1 HETATM 4 O O3G GTP . . . J 4 0.765 -110.691 40.158 1 26.95 ? O3G GTP 217 F 1 HETATM 5 O O3B GTP . . . J 4 1.053 -110.341 37.67 1 24.82 ? O3B GTP 217 F 1 HETATM 6 P PB GTP . . . J 4 0.744 -111.767 36.975 1 30.5 ? PB GTP 217 F 1 HETATM 7 O O1B GTP . . . J 4 -0.547 -112.355 37.488 1 24.63 ? O1B GTP 217 F 1 HETATM 8 O O2B GTP . . . J 4 1.874 -112.751 37.135 1 14.86 ? O2B GTP 217 F 1 HETATM 9 O O3A GTP . . . J 4 0.457 -111.417 35.439 1 28.96 ? O3A GTP 217 F 1 HETATM 10 P PA GTP . . . J 4 -0.612 -112.343 34.678 1 29.71 ? PA GTP 217 F 1 HETATM 11 O O1A GTP . . . J 4 -2.018 -111.932 35.054 1 35.83 ? O1A GTP 217 F 1 HETATM 12 O O2A GTP . . . J 4 -0.341 -113.771 35.084 1 18.7 ? O2A GTP 217 F 1 HETATM 13 O O5' GTP . . . J 4 -0.437 -112.094 33.092 1 19.54 ? O5' GTP 217 F 1 HETATM 14 C C5' GTP . . . J 4 0.821 -112.3 32.488 1 19.26 ? C5' GTP 217 F 1 HETATM 15 C C4' GTP . . . J 4 0.96 -111.558 31.156 1 21.13 ? C4' GTP 217 F 1 HETATM 16 O O4' GTP . . . J 4 2.007 -112.223 30.485 1 16 ? O4' GTP 217 F 1 HETATM 17 C C3' GTP . . . J 4 -0.245 -111.689 30.231 1 17.17 ? C3' GTP 217 F 1 HETATM 18 O O3' GTP . . . J 4 -0.052 -110.848 29.11 1 7.67 ? O3' GTP 217 F 1 HETATM 19 C C2' GTP . . . J 4 -0.086 -113.095 29.745 1 14.21 ? C2' GTP 217 F 1 HETATM 20 O O2' GTP . . . J 4 -0.778 -113.253 28.534 1 9.4 ? O2' GTP 217 F 1 HETATM 21 C C1' GTP . . . J 4 1.419 -113.085 29.531 1 17.16 ? C1' GTP 217 F 1 HETATM 22 N N9 GTP . . . J 4 2.037 -114.379 29.77 1 14.1 ? N9 GTP 217 F 1 HETATM 23 C C8 GTP . . . J 4 1.998 -115.171 30.881 1 12.01 ? C8 GTP 217 F 1 HETATM 24 N N7 GTP . . . J 4 2.752 -116.257 30.617 1 15.11 ? N7 GTP 217 F 1 HETATM 25 C C5 GTP . . . J 4 3.273 -116.151 29.372 1 18.76 ? C5 GTP 217 F 1 HETATM 26 C C6 GTP . . . J 4 4.11 -116.958 28.602 1 18.03 ? C6 GTP 217 F 1 HETATM 27 O O6 GTP . . . J 4 4.548 -118.028 29.03 1 22.04 ? O6 GTP 217 F 1 HETATM 28 N N1 GTP . . . J 4 4.453 -116.548 27.331 1 14.07 ? N1 GTP 217 F 1 HETATM 29 C C2 GTP . . . J 4 3.978 -115.35 26.833 1 17.49 ? C2 GTP 217 F 1 HETATM 30 N N2 GTP . . . J 4 4.312 -114.944 25.611 1 30.24 ? N2 GTP 217 F 1 HETATM 31 N N3 GTP . . . J 4 3.158 -114.557 27.602 1 16.26 ? N3 GTP 217 F 1 HETATM 32 C C4 GTP . . . J 4 2.822 -114.962 28.842 1 16.95 ? C4 GTP 217 F 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #