data_4F38 # _model_server_result.job_id Px227q-tiCizZyztoOSGSg _model_server_result.datetime_utc '2024-11-16 23:32:45' _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 4f38 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":204}' # _entry.id 4F38 # _exptl.entry_id 4F38 _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 4F38 _cell.length_a 46 _cell.length_b 71.576 _cell.length_c 136.03 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4F38 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 covale ? covale1 A SG CYS 192 A CYS 190 1_555 C C1 GER . A GER 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? metalc ? metalc1 A OG1 THR 21 A THR 19 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc2 A O THR 39 A THR 37 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 A OD1 ASP 47 A ASP 45 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.787 ? metalc ? metalc4 A OD2 ASP 47 A ASP 45 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc5 D MG MG . A MG 202 1_555 F O2G GNP . A GNP 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.793 ? metalc ? metalc6 D MG MG . A MG 202 1_555 F O2B GNP . A GNP 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc7 D MG MG . A MG 202 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.924 ? metalc ? metalc8 E MG MG . A MG 203 1_555 G O HOH . A HOH 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? # _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 182 n n PG O2G GNP sing 183 n n PG O3G GNP sing 184 n n PG N3B GNP sing 185 n n O2G HOG2 GNP sing 186 n n O3G HOG3 GNP sing 187 n n N3B PB GNP sing 188 n n N3B HNB3 GNP sing 189 n n PB O1B GNP doub 190 n n PB O2B GNP sing 191 n n PB O3A GNP sing 192 n n O2B HOB2 GNP sing 193 n n O3A PA GNP sing 194 n n PA O1A GNP doub 195 n n PA O2A GNP sing 196 n n PA O5' GNP sing 197 n n O2A HOA2 GNP sing 198 n n O5' C5' GNP sing 199 n n C5' C4' GNP sing 200 n n C5' "H5'2" GNP sing 201 n n C5' "H5'1" GNP sing 202 n n C4' O4' GNP sing 203 n n C4' C3' GNP sing 204 n n C4' H4' GNP sing 205 n n O4' C1' GNP sing 206 n n C3' O3' GNP sing 207 n n C3' C2' GNP sing 208 n n C3' H3' GNP sing 209 n n O3' HO3' GNP sing 210 n n C2' O2' GNP sing 211 n n C2' C1' GNP sing 212 n n C2' H2' GNP sing 213 n n O2' HO2' GNP sing 214 n n C1' N9 GNP sing 215 n n C1' H1' GNP sing 216 n n N9 C8 GNP sing 217 n y N9 C4 GNP sing 218 n y C8 N7 GNP doub 219 n y C8 H8 GNP sing 220 n n N7 C5 GNP sing 221 n y C5 C6 GNP sing 222 n y C5 C4 GNP doub 223 n y C6 O6 GNP doub 224 n n C6 N1 GNP sing 225 n y N1 C2 GNP sing 226 n y N1 HN1 GNP sing 227 n n C2 N2 GNP sing 228 n n C2 N3 GNP doub 229 n y N2 HN21 GNP sing 230 n n N2 HN22 GNP sing 231 n n N3 C4 GNP sing 232 n y # _atom_sites.entry_id 4F38 _atom_sites.fract_transf_matrix[1][1] 0.021739 _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] 0.013971 _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] 0.007351 _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 C 3 GER A 1 201 190 GER CYS . D 4 MG A 1 202 301 MG MG . E 4 MG A 1 203 302 MG MG . F 5 GNP A 1 204 1 GNP GNP . G 6 HOH A 1 301 1 HOH HOH . G 6 HOH A 2 302 3 HOH HOH . G 6 HOH A 3 303 4 HOH HOH . G 6 HOH A 4 304 6 HOH HOH . G 6 HOH A 5 305 11 HOH HOH . G 6 HOH A 6 306 16 HOH HOH . G 6 HOH A 7 307 18 HOH HOH . G 6 HOH A 8 308 21 HOH HOH . G 6 HOH A 9 309 22 HOH HOH . G 6 HOH A 10 310 23 HOH HOH . G 6 HOH A 11 311 30 HOH HOH . G 6 HOH A 12 312 32 HOH HOH . G 6 HOH A 13 313 36 HOH HOH . G 6 HOH A 14 314 39 HOH HOH . G 6 HOH A 15 315 55 HOH HOH . G 6 HOH A 16 316 63 HOH HOH . G 6 HOH A 17 317 69 HOH HOH . G 6 HOH A 18 318 72 HOH HOH . G 6 HOH A 19 319 77 HOH HOH . G 6 HOH A 20 320 90 HOH HOH . G 6 HOH A 21 321 97 HOH HOH . G 6 HOH A 22 322 98 HOH HOH . G 6 HOH A 23 323 100 HOH HOH . G 6 HOH A 24 324 102 HOH HOH . G 6 HOH A 25 325 103 HOH HOH . G 6 HOH A 26 326 104 HOH HOH . G 6 HOH A 27 327 105 HOH HOH . G 6 HOH A 28 328 106 HOH HOH . G 6 HOH A 29 329 112 HOH HOH . G 6 HOH A 30 330 114 HOH HOH . G 6 HOH A 31 331 115 HOH HOH . G 6 HOH A 32 332 116 HOH HOH . G 6 HOH A 33 333 117 HOH HOH . G 6 HOH A 34 334 118 HOH HOH . G 6 HOH A 35 335 119 HOH HOH . H 6 HOH B 1 301 5 HOH HOH . H 6 HOH B 2 302 7 HOH HOH . H 6 HOH B 3 303 8 HOH HOH . H 6 HOH B 4 304 9 HOH HOH . H 6 HOH B 5 305 12 HOH HOH . H 6 HOH B 6 306 14 HOH HOH . H 6 HOH B 7 307 15 HOH HOH . H 6 HOH B 8 308 17 HOH HOH . H 6 HOH B 9 309 19 HOH HOH . H 6 HOH B 10 310 20 HOH HOH . H 6 HOH B 11 311 25 HOH HOH . H 6 HOH B 12 312 26 HOH HOH . H 6 HOH B 13 313 27 HOH HOH . H 6 HOH B 14 314 29 HOH HOH . H 6 HOH B 15 315 35 HOH HOH . H 6 HOH B 16 316 37 HOH HOH . H 6 HOH B 17 317 41 HOH HOH . H 6 HOH B 18 318 42 HOH HOH . H 6 HOH B 19 319 43 HOH HOH . H 6 HOH B 20 320 45 HOH HOH . H 6 HOH B 21 321 50 HOH HOH . H 6 HOH B 22 322 51 HOH HOH . H 6 HOH B 23 323 52 HOH HOH . H 6 HOH B 24 324 53 HOH HOH . H 6 HOH B 25 325 56 HOH HOH . H 6 HOH B 26 326 62 HOH HOH . H 6 HOH B 27 327 64 HOH HOH . H 6 HOH B 28 328 66 HOH HOH . H 6 HOH B 29 329 67 HOH HOH . H 6 HOH B 30 330 68 HOH HOH . H 6 HOH B 31 331 70 HOH HOH . H 6 HOH B 32 332 71 HOH HOH . H 6 HOH B 33 333 73 HOH HOH . H 6 HOH B 34 334 75 HOH HOH . H 6 HOH B 35 335 81 HOH HOH . H 6 HOH B 36 336 82 HOH HOH . H 6 HOH B 37 337 83 HOH HOH . H 6 HOH B 38 338 84 HOH HOH . H 6 HOH B 39 339 86 HOH HOH . H 6 HOH B 40 340 87 HOH HOH . H 6 HOH B 41 341 92 HOH HOH . H 6 HOH B 42 342 95 HOH HOH . H 6 HOH B 43 343 96 HOH HOH . H 6 HOH B 44 344 113 HOH HOH . H 6 HOH B 45 345 122 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 . . . F 5 -20.805 -18.821 23.207 1 52.48 ? PG GNP 204 A 1 HETATM 2 O O1G GNP . . . F 5 -19.735 -18.058 22.447 1 53.76 ? O1G GNP 204 A 1 HETATM 3 O O2G GNP . . . F 5 -21.931 -17.886 23.58 1 49.34 ? O2G GNP 204 A 1 HETATM 4 O O3G GNP . . . F 5 -21.248 -19.976 22.316 1 55.69 ? O3G GNP 204 A 1 HETATM 5 N N3B GNP . . . F 5 -20.218 -19.511 24.549 1 44.37 ? N3B GNP 204 A 1 HETATM 6 P PB GNP . . . F 5 -19.847 -18.714 25.877 1 35.9 ? PB GNP 204 A 1 HETATM 7 O O1B GNP . . . F 5 -18.496 -18.16 25.782 1 34.01 ? O1B GNP 204 A 1 HETATM 8 O O2B GNP . . . F 5 -20.926 -17.722 25.977 1 35.54 ? O2B GNP 204 A 1 HETATM 9 O O3A GNP . . . F 5 -19.869 -19.594 27.129 1 32.22 ? O3A GNP 204 A 1 HETATM 10 P PA GNP . . . F 5 -21.15 -20.165 27.734 1 30.49 ? PA GNP 204 A 1 HETATM 11 O O1A GNP . . . F 5 -21.332 -19.626 29.083 1 25.48 ? O1A GNP 204 A 1 HETATM 12 O O2A GNP . . . F 5 -22.251 -20.034 26.765 1 32 ? O2A GNP 204 A 1 HETATM 13 O O5' GNP . . . F 5 -21.122 -21.714 27.953 1 33.87 ? O5' GNP 204 A 1 HETATM 14 C C5' GNP . . . F 5 -20.003 -22.596 27.857 1 37.56 ? C5' GNP 204 A 1 HETATM 15 C C4' GNP . . . F 5 -20.396 -23.921 28.512 1 39.3 ? C4' GNP 204 A 1 HETATM 16 O O4' GNP . . . F 5 -19.619 -24.141 29.72 1 38.63 ? O4' GNP 204 A 1 HETATM 17 C C3' GNP . . . F 5 -21.86 -23.972 28.955 1 39.63 ? C3' GNP 204 A 1 HETATM 18 O O3' GNP . . . F 5 -22.474 -25.207 28.582 1 44.09 ? O3' GNP 204 A 1 HETATM 19 C C2' GNP . . . F 5 -21.866 -23.824 30.466 1 36.76 ? C2' GNP 204 A 1 HETATM 20 O O2' GNP . . . F 5 -22.676 -24.819 31.044 1 40.16 ? O2' GNP 204 A 1 HETATM 21 C C1' GNP . . . F 5 -20.438 -24.106 30.881 1 36.55 ? C1' GNP 204 A 1 HETATM 22 N N9 GNP . . . F 5 -19.926 -23.169 31.892 1 35.27 ? N9 GNP 204 A 1 HETATM 23 C C8 GNP . . . F 5 -19.887 -21.805 31.854 1 34.95 ? C8 GNP 204 A 1 HETATM 24 N N7 GNP . . . F 5 -19.371 -21.259 32.926 1 34.24 ? N7 GNP 204 A 1 HETATM 25 C C5 GNP . . . F 5 -19.038 -22.325 33.736 1 33.11 ? C5 GNP 204 A 1 HETATM 26 C C6 GNP . . . F 5 -18.442 -22.365 35.026 1 32.61 ? C6 GNP 204 A 1 HETATM 27 O O6 GNP . . . F 5 -18.064 -21.445 35.752 1 31.57 ? O6 GNP 204 A 1 HETATM 28 N N1 GNP . . . F 5 -18.281 -23.664 35.481 1 34.02 ? N1 GNP 204 A 1 HETATM 29 C C2 GNP . . . F 5 -18.644 -24.783 34.766 1 34.38 ? C2 GNP 204 A 1 HETATM 30 N N2 GNP . . . F 5 -18.429 -25.965 35.345 1 36.89 ? N2 GNP 204 A 1 HETATM 31 N N3 GNP . . . F 5 -19.209 -24.761 33.58 1 34.51 ? N3 GNP 204 A 1 HETATM 32 C C4 GNP . . . F 5 -19.376 -23.502 33.113 1 34.58 ? C4 GNP 204 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 440 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #