data_6V65 # _model_server_result.job_id JdTNCkmlPwypQ0Q5dohyjA _model_server_result.datetime_utc '2024-11-04 20:56:31' _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 6v65 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 6V65 # _exptl.entry_id 6V65 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 99.61 _cell.angle_gamma 90 _cell.entry_id 6V65 _cell.length_a 72.556 _cell.length_b 70.553 _cell.length_c 80.311 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V65 _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,C,F,G,H,I,J,K,L 1 1 A,D,E 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_645 -x+1,y-1/2,-z -1 0 0 0 1 0 0 0 -1 72.556 -35.2765 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _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 ND1 HIS 37 A HIS 49 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc2 A SG CYS 43 A CYS 55 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 D ZN ZN . A ZN 201 2_645 B NE2 HIS 230 B HIS 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc4 D ZN ZN . A ZN 201 2_645 B OD1 ASP 251 B ASP 1452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc5 C OG SER 18 C SER 17 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc6 C OG1 THR 36 C THR 35 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc7 G O3G GNP . C GNP 501 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc8 G O1B GNP . C GNP 501 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 GNP doub 133 n n PG O2G GNP sing 134 n n PG O3G GNP sing 135 n n PG N3B GNP sing 136 n n O2G HOG2 GNP sing 137 n n O3G HOG3 GNP sing 138 n n N3B PB GNP sing 139 n n N3B HNB3 GNP sing 140 n n PB O1B GNP doub 141 n n PB O2B GNP sing 142 n n PB O3A GNP sing 143 n n O2B HOB2 GNP sing 144 n n O3A PA GNP sing 145 n n PA O1A GNP doub 146 n n PA O2A GNP sing 147 n n PA O5' GNP sing 148 n n O2A HOA2 GNP sing 149 n n O5' C5' GNP sing 150 n n C5' C4' GNP sing 151 n n C5' "H5'2" GNP sing 152 n n C5' "H5'1" GNP sing 153 n n C4' O4' GNP sing 154 n n C4' C3' GNP sing 155 n n C4' H4' GNP sing 156 n n O4' C1' GNP sing 157 n n C3' O3' GNP sing 158 n n C3' C2' GNP sing 159 n n C3' H3' GNP sing 160 n n O3' HO3' GNP sing 161 n n C2' O2' GNP sing 162 n n C2' C1' GNP sing 163 n n C2' H2' GNP sing 164 n n O2' HO2' GNP sing 165 n n C1' N9 GNP sing 166 n n C1' H1' GNP sing 167 n n N9 C8 GNP sing 168 n y N9 C4 GNP sing 169 n y C8 N7 GNP doub 170 n y C8 H8 GNP sing 171 n n N7 C5 GNP sing 172 n y C5 C6 GNP sing 173 n y C5 C4 GNP doub 174 n y C6 O6 GNP doub 175 n n C6 N1 GNP sing 176 n y N1 C2 GNP sing 177 n y N1 HN1 GNP sing 178 n n C2 N2 GNP sing 179 n n C2 N3 GNP doub 180 n y N2 HN21 GNP sing 181 n n N2 HN22 GNP sing 182 n n N3 C4 GNP sing 183 n y # _atom_sites.entry_id 6V65 _atom_sites.fract_transf_matrix[1][1] 0.013782 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002333 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014174 _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] 0.012629 _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 ZN A 1 201 2 ZN ZN . E 5 FMT A 1 202 4 FMT FMT . F 5 FMT B 1 1601 1 FMT FMT . G 6 GNP C 1 501 501 GNP GNP . H 7 MG C 1 502 1 MG MG . I 5 FMT C 1 503 2 FMT FMT . J 5 FMT C 1 504 3 FMT FMT . K 8 HOH B 1 1701 3 HOH HOH . K 8 HOH B 2 1702 4 HOH HOH . L 8 HOH C 1 601 1 HOH HOH . L 8 HOH C 2 602 5 HOH HOH . L 8 HOH C 3 603 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 PG GNP . . . G 6 4.943 10.276 27.932 1 72.51 ? PG GNP 501 C 1 HETATM 2 O O1G GNP . . . G 6 5.478 10.554 26.595 1 45.27 ? O1G GNP 501 C 1 HETATM 3 O O2G GNP . . . G 6 4.012 11.363 28.237 1 60.14 ? O2G GNP 501 C 1 HETATM 4 O O3G GNP . . . G 6 4.191 8.992 27.936 1 72.72 ? O3G GNP 501 C 1 HETATM 5 N N3B GNP . . . G 6 6.078 10.236 29.061 1 61.7 ? N3B GNP 501 C 1 HETATM 6 P PB GNP . . . G 6 5.658 9.562 30.445 1 59.73 ? PB GNP 501 C 1 HETATM 7 O O1B GNP . . . G 6 5.141 8.191 30.157 1 84.66 ? O1B GNP 501 C 1 HETATM 8 O O2B GNP . . . G 6 4.873 10.46 31.331 1 71.31 ? O2B GNP 501 C 1 HETATM 9 O O3A GNP . . . G 6 6.928 9.233 31.303 1 59.27 ? O3A GNP 501 C 1 HETATM 10 P PA GNP . . . G 6 7.467 7.766 31.493 1 72.71 ? PA GNP 501 C 1 HETATM 11 O O1A GNP . . . G 6 7.675 7.183 30.151 1 58.42 ? O1A GNP 501 C 1 HETATM 12 O O2A GNP . . . G 6 6.576 7.048 32.428 1 75.8 ? O2A GNP 501 C 1 HETATM 13 O O5' GNP . . . G 6 8.847 8.034 32.211 1 56.94 ? O5' GNP 501 C 1 HETATM 14 C C5' GNP . . . G 6 9.814 8.827 31.52 1 54.91 ? C5' GNP 501 C 1 HETATM 15 C C4' GNP . . . G 6 11.106 8.724 32.28 1 65.65 ? C4' GNP 501 C 1 HETATM 16 O O4' GNP . . . G 6 10.826 9.074 33.654 1 69.85 ? O4' GNP 501 C 1 HETATM 17 C C3' GNP . . . G 6 11.747 7.333 32.339 1 74.17 ? C3' GNP 501 C 1 HETATM 18 O O3' GNP . . . G 6 13.155 7.487 32.334 1 78.18 ? O3' GNP 501 C 1 HETATM 19 C C2' GNP . . . G 6 11.381 6.863 33.744 1 65.49 ? C2' GNP 501 C 1 HETATM 20 O O2' GNP . . . G 6 12.265 5.881 34.23 1 56.41 ? O2' GNP 501 C 1 HETATM 21 C C1' GNP . . . G 6 11.479 8.175 34.506 1 63.31 ? C1' GNP 501 C 1 HETATM 22 N N9 GNP . . . G 6 10.731 8.163 35.753 1 59.27 ? N9 GNP 501 C 1 HETATM 23 C C8 GNP . . . G 6 9.371 8.055 35.855 1 60.03 ? C8 GNP 501 C 1 HETATM 24 N N7 GNP . . . G 6 8.941 8.076 37.088 1 59.7 ? N7 GNP 501 C 1 HETATM 25 C C5 GNP . . . G 6 10.088 8.223 37.846 1 58.78 ? C5 GNP 501 C 1 HETATM 26 C C6 GNP . . . G 6 10.23 8.317 39.248 1 60.85 ? C6 GNP 501 C 1 HETATM 27 O O6 GNP . . . G 6 9.342 8.281 40.104 1 59.49 ? O6 GNP 501 C 1 HETATM 28 N N1 GNP . . . G 6 11.561 8.467 39.623 1 56.84 ? N1 GNP 501 C 1 HETATM 29 C C2 GNP . . . G 6 12.609 8.519 38.743 1 55.42 ? C2 GNP 501 C 1 HETATM 30 N N2 GNP . . . G 6 13.82 8.663 39.284 1 64.31 ? N2 GNP 501 C 1 HETATM 31 N N3 GNP . . . G 6 12.483 8.432 37.421 1 49.6 ? N3 GNP 501 C 1 HETATM 32 C C4 GNP . . . G 6 11.197 8.283 37.038 1 57.76 ? C4 GNP 501 C 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #