data_7KDC # _model_server_result.job_id '_Cs-AiTLCrNeyO54TlI7oA' _model_server_result.datetime_utc '2025-02-20 19:41:30' _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 7kdc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 7KDC # _exptl.entry_id 7KDC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 90 _cell.angle_gamma 120 _cell.entry_id 7KDC _cell.length_a 82.81 _cell.length_b 82.81 _cell.length_c 136.761 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KDC _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall 'P 31' _symmetry.space_group_name_H-M 'P 31' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,C,E,F,G,K,M 1 1 B,D,H,I,J,L,N 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 ? 3 E N N ? 3 H 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 disulf ? disulf1 C SG CYS 46 C CYS 1508 1_555 D SG CYS 48 D CYS 1510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 C SG CYS 48 C CYS 1510 1_555 D SG CYS 46 D CYS 1508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A OG1 THR 28 A THR 31 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc2 A OG1 THR 46 A THR 49 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc3 E O2G GNP . A GNP 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc4 E O2B GNP . A GNP 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc5 F MG MG . A MG 202 1_555 K O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc6 B OG1 THR 28 B THR 31 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc7 B OG1 THR 46 B THR 49 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc8 H O2G GNP . B GNP 201 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc9 H O2B GNP . B GNP 201 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc10 I MG MG . B MG 202 1_555 L O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? # _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 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 7KDC _atom_sites.fract_transf_matrix[1][1] 0.012076 _atom_sites.fract_transf_matrix[1][2] 0.006972 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013944 _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] 0.007312 _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 E 3 GNP A 1 201 201 GNP GNP . F 4 MG A 1 202 202 MG MG . G 4 MG A 1 203 1 MG MG . H 3 GNP B 1 201 201 GNP GNP . I 4 MG B 1 202 202 MG MG . J 4 MG B 1 203 2 MG MG . K 5 HOH A 1 301 11 HOH HOH . K 5 HOH A 2 302 10 HOH HOH . K 5 HOH A 3 303 1 HOH HOH . L 5 HOH B 1 301 12 HOH HOH . L 5 HOH B 2 302 8 HOH HOH . L 5 HOH B 3 303 2 HOH HOH . M 5 HOH C 1 1901 14 HOH HOH . N 5 HOH D 1 1901 15 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 . . . E 3 -18.554 53.271 -1.692 1 107.62 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . E 3 -17.224 52.586 -1.81 1 100.72 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . E 3 -18.403 54.748 -2.057 1 97.98 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . E 3 -19.565 52.596 -2.659 1 113.23 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . E 3 -19.135 53.136 -0.091 1 113.8 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . E 3 -18.194 53.609 1.166 1 111.49 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . E 3 -16.996 52.701 1.278 1 100.38 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . E 3 -17.74 55.026 0.939 1 110.89 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . E 3 -19.061 53.532 2.56 1 114.03 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . E 3 -19.731 54.81 3.227 1 116.22 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . E 3 -18.62 55.574 3.943 1 121.98 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . E 3 -20.512 55.588 2.241 1 114.67 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . E 3 -20.688 54.192 4.313 1 108.94 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . E 3 -21.411 52.969 4.066 1 109.7 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . E 3 -22.468 52.778 5.129 1 120.37 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . E 3 -21.853 52.321 6.354 1 121.63 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . E 3 -23.284 54.017 5.495 1 123.29 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . E 3 -24.645 53.679 5.739 1 119.22 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . E 3 -22.582 54.532 6.755 1 126.08 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . E 3 -23.473 55.233 7.615 1 135.79 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . E 3 -22.122 53.227 7.408 1 127.35 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . E 3 -20.897 53.378 8.21 1 126.73 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . E 3 -19.682 53.846 7.782 1 120.24 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . E 3 -18.771 53.866 8.728 1 114 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . E 3 -19.429 53.381 9.846 1 121.13 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . E 3 -18.97 53.162 11.198 1 113.4 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . E 3 -17.845 53.374 11.649 1 110.09 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . E 3 -19.969 52.657 12.005 1 115.7 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . E 3 -21.25 52.386 11.602 1 118.89 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . E 3 -22.083 51.901 12.524 1 134.75 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . E 3 -21.687 52.583 10.359 1 114.69 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . E 3 -20.738 53.076 9.542 1 127.53 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 87 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 413 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #