data_6VC8 # _model_server_result.job_id kSO8NjftFB5DDKL06sqxjg _model_server_result.datetime_utc '2025-06-27 06:59:48' _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 6vc8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1001}' # _entry.id 6VC8 # _exptl.entry_id 6VC8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 112.92 _cell.angle_gamma 90 _cell.entry_id 6VC8 _cell.length_a 69.21 _cell.length_b 82.33 _cell.length_c 88.14 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VC8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,J 1 1 B,F,G,K 2 1 C,H,I,L 3 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 ? 2 D N N ? 2 F N N ? 2 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 metalc ? metalc1 A OG SER 18 A SER 17 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc2 A OG1 THR 36 A THR 35 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc3 D O1G GNP . A GNP 1001 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc4 D O2B GNP . A GNP 1001 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc5 E MG MG . A MG 1002 1_555 J O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc6 E MG MG . A MG 1002 1_555 J O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc7 B OG SER 18 B SER 17 1_555 G MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc8 B OG1 THR 36 B THR 35 1_555 G MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc9 F O1G GNP . B GNP 1001 1_555 G MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc10 F O2B GNP . B GNP 1001 1_555 G MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc11 G MG MG . B MG 1002 1_555 K O HOH . B HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc12 G MG MG . B MG 1002 1_555 K O HOH . B HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc13 C OG SER 18 C SER 17 1_555 I MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc14 H O1G GNP . C GNP 1001 1_555 I MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc15 H O2B GNP . C GNP 1001 1_555 I MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc16 I MG MG . C MG 1002 1_555 L O HOH . C HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc17 I MG MG . C MG 1002 1_555 L O HOH . C HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc18 I MG MG . C MG 1002 1_555 L O HOH . C HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? # _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 6VC8 _atom_sites.fract_transf_matrix[1][1] 0.014449 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00611 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012146 _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] 0.012318 _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 2 GNP A 1 1001 1001 GNP GNP . E 3 MG A 1 1002 1002 MG MG . F 2 GNP B 1 1001 1001 GNP GNP . G 3 MG B 1 1002 1002 MG MG . H 2 GNP C 1 1001 1001 GNP GNP . I 3 MG C 1 1002 1002 MG MG . J 4 HOH A 1 1101 15 HOH HOH . J 4 HOH A 2 1102 4 HOH HOH . J 4 HOH A 3 1103 14 HOH HOH . J 4 HOH A 4 1104 3 HOH HOH . J 4 HOH A 5 1105 2 HOH HOH . J 4 HOH A 6 1106 20 HOH HOH . J 4 HOH A 7 1107 1 HOH HOH . J 4 HOH A 8 1108 21 HOH HOH . J 4 HOH A 9 1109 5 HOH HOH . J 4 HOH A 10 1110 18 HOH HOH . J 4 HOH A 11 1111 19 HOH HOH . J 4 HOH A 12 1112 11 HOH HOH . J 4 HOH A 13 1113 26 HOH HOH . K 4 HOH B 1 1101 8 HOH HOH . K 4 HOH B 2 1102 6 HOH HOH . K 4 HOH B 3 1103 10 HOH HOH . K 4 HOH B 4 1104 7 HOH HOH . K 4 HOH B 5 1105 9 HOH HOH . K 4 HOH B 6 1106 23 HOH HOH . L 4 HOH C 1 1101 16 HOH HOH . L 4 HOH C 2 1102 13 HOH HOH . L 4 HOH C 3 1103 17 HOH HOH . L 4 HOH C 4 1104 27 HOH HOH . L 4 HOH C 5 1105 22 HOH HOH . L 4 HOH C 6 1106 25 HOH HOH . L 4 HOH C 7 1107 12 HOH HOH . L 4 HOH C 8 1108 28 HOH HOH . L 4 HOH C 9 1109 24 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 . . . H 2 22.227 -7.877 38.218 1 80.66 ? PG GNP 1001 C 1 HETATM 2 O O1G GNP . . . H 2 22.541 -8.603 39.511 1 84.76 ? O1G GNP 1001 C 1 HETATM 3 O O2G GNP . . . H 2 22.479 -6.382 38.315 1 77.39 ? O2G GNP 1001 C 1 HETATM 4 O O3G GNP . . . H 2 20.836 -8.328 37.843 1 77.51 ? O3G GNP 1001 C 1 HETATM 5 N N3B GNP . . . H 2 23.101 -8.487 37.034 1 72.23 ? N3B GNP 1001 C 1 HETATM 6 P PB GNP . . . H 2 24.656 -8.81 37.106 1 67.1 ? PB GNP 1001 C 1 HETATM 7 O O1B GNP . . . H 2 25.431 -7.685 36.542 1 64.95 ? O1B GNP 1001 C 1 HETATM 8 O O2B GNP . . . H 2 24.987 -9.315 38.465 1 62.63 ? O2B GNP 1001 C 1 HETATM 9 O O3A GNP . . . H 2 24.869 -9.965 36.141 1 70.55 ? O3A GNP 1001 C 1 HETATM 10 P PA GNP . . . H 2 24.85 -11.414 36.603 1 67.32 ? PA GNP 1001 C 1 HETATM 11 O O1A GNP . . . H 2 26.196 -11.752 37.125 1 66.68 ? O1A GNP 1001 C 1 HETATM 12 O O2A GNP . . . H 2 23.657 -11.642 37.444 1 65.1 ? O2A GNP 1001 C 1 HETATM 13 O O5' GNP . . . H 2 24.688 -12.293 35.317 1 56.01 ? O5' GNP 1001 C 1 HETATM 14 C C5' GNP . . . H 2 23.548 -12.196 34.498 1 54.58 ? C5' GNP 1001 C 1 HETATM 15 C C4' GNP . . . H 2 23.632 -13.31 33.474 1 62.91 ? C4' GNP 1001 C 1 HETATM 16 O O4' GNP . . . H 2 24.851 -13.175 32.697 1 64.4 ? O4' GNP 1001 C 1 HETATM 17 C C3' GNP . . . H 2 23.706 -14.729 34.031 1 71.02 ? C3' GNP 1001 C 1 HETATM 18 O O3' GNP . . . H 2 23.05 -15.611 33.112 1 79.85 ? O3' GNP 1001 C 1 HETATM 19 C C2' GNP . . . H 2 25.212 -15.002 34.098 1 65.61 ? C2' GNP 1001 C 1 HETATM 20 O O2' GNP . . . H 2 25.523 -16.378 34.142 1 69.95 ? O2' GNP 1001 C 1 HETATM 21 C C1' GNP . . . H 2 25.644 -14.351 32.785 1 57.96 ? C1' GNP 1001 C 1 HETATM 22 N N9 GNP . . . H 2 27.037 -13.911 32.656 1 45.99 ? N9 GNP 1001 C 1 HETATM 23 C C8 GNP . . . H 2 27.756 -13.046 33.458 1 40.61 ? C8 GNP 1001 C 1 HETATM 24 N N7 GNP . . . H 2 28.992 -12.853 33.053 1 37.01 ? N7 GNP 1001 C 1 HETATM 25 C C5 GNP . . . H 2 29.085 -13.637 31.922 1 37.56 ? C5 GNP 1001 C 1 HETATM 26 C C6 GNP . . . H 2 30.17 -13.83 31.051 1 41.69 ? C6 GNP 1001 C 1 HETATM 27 O O6 GNP . . . H 2 31.288 -13.326 31.11 1 50.29 ? O6 GNP 1001 C 1 HETATM 28 N N1 GNP . . . H 2 29.863 -14.709 30.019 1 41.23 ? N1 GNP 1001 C 1 HETATM 29 C C2 GNP . . . H 2 28.636 -15.313 29.85 1 46.45 ? C2 GNP 1001 C 1 HETATM 30 N N2 GNP . . . H 2 28.532 -16.118 28.785 1 53.04 ? N2 GNP 1001 C 1 HETATM 31 N N3 GNP . . . H 2 27.594 -15.144 30.66 1 41.58 ? N3 GNP 1001 C 1 HETATM 32 C C4 GNP . . . H 2 27.897 -14.285 31.659 1 42.12 ? C4 GNP 1001 C 1 # _model_server_stats.io_time_ms 257 _model_server_stats.parse_time_ms 74 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 32 #