data_1NVW # _model_server_result.job_id lMVxhoyJgQsnu320K59T8A _model_server_result.datetime_utc '2024-10-15 08:22:14' _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 1nvw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1001}' # _entry.id 1NVW # _exptl.entry_id 1NVW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 5 _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 90 _cell.angle_gamma 90 _cell.entry_id 1NVW _cell.length_a 184.046 _cell.length_b 184.046 _cell.length_c 178.943 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NVW _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 2 2' # 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 24-meric 24 software_defined_assembly 2 PISA dodecameric 12 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 2 1,2,3,4,5,6,7,8 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 3 1,2,3,4 # 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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 178.943 6 'crystal symmetry operation' 6_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 178.943 7 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 178.943 8 'crystal symmetry operation' 8_556 -y,-x,-z+1 0 -1 0 -1 0 0 0 0 -1 0 0 178.943 # _struct_asym.details ? _struct_asym.entity_id 5 _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 OG SER 17 Q SER 17 1_555 D MG MG . Q MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc2 A OG1 THR 35 Q THR 35 1_555 D MG MG . Q MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc3 G O2G GNP . Q GNP 1001 1_555 D MG MG . Q MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc4 G O2B GNP . Q GNP 1001 1_555 D MG MG . Q MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc5 D MG MG . Q MG 1002 1_555 M O HOH . Q HOH 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? # _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 1NVW _atom_sites.fract_transf_matrix[1][1] 0.005433 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005433 _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] 0.005588 _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 3 MG Q 1 1002 2 MG MG . E 4 PO4 Q 1 1008 8 PO4 PO4 . F 4 PO4 Q 1 1009 9 PO4 PO4 . G 5 GNP Q 1 1001 1 GNP GNP . H 4 PO4 R 1 1003 3 PO4 PO4 . I 4 PO4 S 1 1047 4 PO4 PO4 . J 4 PO4 S 1 1048 5 PO4 PO4 . K 4 PO4 S 1 1049 6 PO4 PO4 . L 4 PO4 S 1 1050 7 PO4 PO4 . M 6 HOH Q 1 1010 1 HOH HOH . M 6 HOH Q 2 1011 7 HOH HOH . M 6 HOH Q 3 1012 25 HOH HOH . M 6 HOH Q 4 1013 29 HOH HOH . M 6 HOH Q 5 1014 40 HOH HOH . M 6 HOH Q 6 1015 44 HOH HOH . M 6 HOH Q 7 1016 51 HOH HOH . M 6 HOH Q 8 1017 54 HOH HOH . N 6 HOH R 1 1004 2 HOH HOH . N 6 HOH R 2 1005 11 HOH HOH . N 6 HOH R 3 1006 17 HOH HOH . N 6 HOH R 4 1007 20 HOH HOH . N 6 HOH R 5 1008 22 HOH HOH . N 6 HOH R 6 1009 28 HOH HOH . N 6 HOH R 7 1010 42 HOH HOH . N 6 HOH R 8 1011 43 HOH HOH . N 6 HOH R 9 1012 45 HOH HOH . N 6 HOH R 10 1013 52 HOH HOH . O 6 HOH S 1 3 3 HOH HOH . O 6 HOH S 2 4 4 HOH HOH . O 6 HOH S 3 5 5 HOH HOH . O 6 HOH S 4 6 6 HOH HOH . O 6 HOH S 5 8 8 HOH HOH . O 6 HOH S 6 9 9 HOH HOH . O 6 HOH S 7 10 10 HOH HOH . O 6 HOH S 8 12 12 HOH HOH . O 6 HOH S 9 13 13 HOH HOH . O 6 HOH S 10 14 14 HOH HOH . O 6 HOH S 11 15 15 HOH HOH . O 6 HOH S 12 16 16 HOH HOH . O 6 HOH S 13 18 18 HOH HOH . O 6 HOH S 14 19 19 HOH HOH . O 6 HOH S 15 21 21 HOH HOH . O 6 HOH S 16 23 23 HOH HOH . O 6 HOH S 17 24 24 HOH HOH . O 6 HOH S 18 26 26 HOH HOH . O 6 HOH S 19 27 27 HOH HOH . O 6 HOH S 20 30 30 HOH HOH . O 6 HOH S 21 31 31 HOH HOH . O 6 HOH S 22 32 32 HOH HOH . O 6 HOH S 23 33 33 HOH HOH . O 6 HOH S 24 34 34 HOH HOH . O 6 HOH S 25 35 35 HOH HOH . O 6 HOH S 26 36 36 HOH HOH . O 6 HOH S 27 37 37 HOH HOH . O 6 HOH S 28 38 38 HOH HOH . O 6 HOH S 29 39 39 HOH HOH . O 6 HOH S 30 41 41 HOH HOH . O 6 HOH S 31 46 46 HOH HOH . O 6 HOH S 32 47 47 HOH HOH . O 6 HOH S 33 48 48 HOH HOH . O 6 HOH S 34 49 49 HOH HOH . O 6 HOH S 35 50 50 HOH HOH . O 6 HOH S 36 53 53 HOH HOH . O 6 HOH S 37 55 55 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 5 14.435 51.305 70.307 1 48.54 ? PG GNP 1001 Q 1 HETATM 2 O O1G GNP . . . G 5 13.195 51.294 71.15 1 51.47 ? O1G GNP 1001 Q 1 HETATM 3 O O2G GNP . . . G 5 14.524 50.052 69.465 1 48.6 ? O2G GNP 1001 Q 1 HETATM 4 O O3G GNP . . . G 5 15.66 51.47 71.107 1 48.92 ? O3G GNP 1001 Q 1 HETATM 5 N N3B GNP . . . G 5 14.148 52.656 69.26 1 45.61 ? N3B GNP 1001 Q 1 HETATM 6 P PB GNP . . . G 5 15.237 53.133 68.068 1 42.73 ? PB GNP 1001 Q 1 HETATM 7 O O1B GNP . . . G 5 16.285 53.962 68.666 1 42.78 ? O1B GNP 1001 Q 1 HETATM 8 O O2B GNP . . . G 5 15.642 51.904 67.313 1 41.87 ? O2B GNP 1001 Q 1 HETATM 9 O O3A GNP . . . G 5 14.316 54.064 67.132 1 40.62 ? O3A GNP 1001 Q 1 HETATM 10 P PA GNP . . . G 5 13.662 53.762 65.77 1 42.44 ? PA GNP 1001 Q 1 HETATM 11 O O1A GNP . . . G 5 14.676 53.552 64.732 1 43.45 ? O1A GNP 1001 Q 1 HETATM 12 O O2A GNP . . . G 5 12.629 52.669 66.01 1 44.91 ? O2A GNP 1001 Q 1 HETATM 13 O O5' GNP . . . G 5 12.945 55.051 65.473 1 40.75 ? O5' GNP 1001 Q 1 HETATM 14 C C5' GNP . . . G 5 11.896 55.536 66.322 1 41.91 ? C5' GNP 1001 Q 1 HETATM 15 C C4' GNP . . . G 5 11.101 56.553 65.583 1 43.13 ? C4' GNP 1001 Q 1 HETATM 16 O O4' GNP . . . G 5 11.813 57.639 65.096 1 42.95 ? O4' GNP 1001 Q 1 HETATM 17 C C3' GNP . . . G 5 10.368 55.944 64.353 1 42.84 ? C3' GNP 1001 Q 1 HETATM 18 O O3' GNP . . . G 5 8.999 56.398 64.285 1 40.61 ? O3' GNP 1001 Q 1 HETATM 19 C C2' GNP . . . G 5 11.222 56.448 63.183 1 43.31 ? C2' GNP 1001 Q 1 HETATM 20 O O2' GNP . . . G 5 10.557 56.504 61.958 1 42.83 ? O2' GNP 1001 Q 1 HETATM 21 C C1' GNP . . . G 5 11.634 57.795 63.715 1 44.23 ? C1' GNP 1001 Q 1 HETATM 22 N N9 GNP . . . G 5 12.909 58.245 63.113 1 46.54 ? N9 GNP 1001 Q 1 HETATM 23 C C8 GNP . . . G 5 14.163 57.496 63.212 1 47.3 ? C8 GNP 1001 Q 1 HETATM 24 N N7 GNP . . . G 5 15.123 58.129 62.581 1 47.86 ? N7 GNP 1001 Q 1 HETATM 25 C C5 GNP . . . G 5 14.472 59.353 62.042 1 47.44 ? C5 GNP 1001 Q 1 HETATM 26 C C6 GNP . . . G 5 15.05 60.437 61.245 1 48.56 ? C6 GNP 1001 Q 1 HETATM 27 O O6 GNP . . . G 5 16.15 60.575 60.86 1 48.97 ? O6 GNP 1001 Q 1 HETATM 28 N N1 GNP . . . G 5 14.095 61.403 60.945 1 50.13 ? N1 GNP 1001 Q 1 HETATM 29 C C2 GNP . . . G 5 12.799 61.236 61.397 1 49.45 ? C2 GNP 1001 Q 1 HETATM 30 N N2 GNP . . . G 5 12.003 62.35 60.966 1 48.59 ? N2 GNP 1001 Q 1 HETATM 31 N N3 GNP . . . G 5 12.21 60.319 62.094 1 48.55 ? N3 GNP 1001 Q 1 HETATM 32 C C4 GNP . . . G 5 13.153 59.367 62.392 1 47.42 ? C4 GNP 1001 Q 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #