data_6XGV # _model_server_result.job_id gAGMaTHYrwt8W1MpGUakYQ _model_server_result.datetime_utc '2024-10-19 15:46:42' _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 6xgv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 6XGV # _exptl.entry_id 6XGV _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 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 120 _cell.entry_id 6XGV _cell.length_a 132.75 _cell.length_b 132.75 _cell.length_c 89.48 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XGV _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6 2 2' # _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,I,J,K,L _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 3 _struct_asym.id C _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 B C GLU 43 B GLU 94 1_555 B N CAF 44 B CAF 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 B C CAF 44 B CAF 95 1_555 B N CYS 45 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc2 A OG1 THR 36 A THR 35 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc3 A NE2 HIS 96 A HIS 95 1_555 E ZN ZN . A ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc4 A NE2 HIS 96 A HIS 95 1_555 E ZN ZN . A ZN 203 12_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc5 C O2G GNP . A GNP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc6 C O1B GNP . A GNP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc7 D MG MG . A MG 202 1_555 K O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc8 D MG MG . A MG 202 1_555 K O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc9 B ND1 HIS 88 B HIS 139 1_555 I ZN ZN . B ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc10 B SG CYS 101 B CYS 152 1_555 J ZN ZN . B ZN 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc11 B SG CYS 104 B CYS 155 1_555 J ZN ZN . B ZN 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc12 B SG CYS 114 B CYS 165 1_555 I ZN ZN . B ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc13 B SG CYS 117 B CYS 168 1_555 I ZN ZN . B ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc14 B ND1 HIS 122 B HIS 173 1_555 J ZN ZN . B ZN 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc15 B SG CYS 125 B CYS 176 1_555 J ZN ZN . B ZN 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc16 B SG CYS 133 B CYS 184 1_555 I ZN ZN . B ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? # _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 151 n n PG O2G GNP sing 152 n n PG O3G GNP sing 153 n n PG N3B GNP sing 154 n n O2G HOG2 GNP sing 155 n n O3G HOG3 GNP sing 156 n n N3B PB GNP sing 157 n n N3B HNB3 GNP sing 158 n n PB O1B GNP doub 159 n n PB O2B GNP sing 160 n n PB O3A GNP sing 161 n n O2B HOB2 GNP sing 162 n n O3A PA GNP sing 163 n n PA O1A GNP doub 164 n n PA O2A GNP sing 165 n n PA O5' GNP sing 166 n n O2A HOA2 GNP sing 167 n n O5' C5' GNP sing 168 n n C5' C4' GNP sing 169 n n C5' "H5'2" GNP sing 170 n n C5' "H5'1" GNP sing 171 n n C4' O4' GNP sing 172 n n C4' C3' GNP sing 173 n n C4' H4' GNP sing 174 n n O4' C1' GNP sing 175 n n C3' O3' GNP sing 176 n n C3' C2' GNP sing 177 n n C3' H3' GNP sing 178 n n O3' HO3' GNP sing 179 n n C2' O2' GNP sing 180 n n C2' C1' GNP sing 181 n n C2' H2' GNP sing 182 n n O2' HO2' GNP sing 183 n n C1' N9 GNP sing 184 n n C1' H1' GNP sing 185 n n N9 C8 GNP sing 186 n y N9 C4 GNP sing 187 n y C8 N7 GNP doub 188 n y C8 H8 GNP sing 189 n n N7 C5 GNP sing 190 n y C5 C6 GNP sing 191 n y C5 C4 GNP doub 192 n y C6 O6 GNP doub 193 n n C6 N1 GNP sing 194 n y N1 C2 GNP sing 195 n y N1 HN1 GNP sing 196 n n C2 N2 GNP sing 197 n n C2 N3 GNP doub 198 n y N2 HN21 GNP sing 199 n n N2 HN22 GNP sing 200 n n N3 C4 GNP sing 201 n y # _atom_sites.entry_id 6XGV _atom_sites.fract_transf_matrix[1][1] 0.007533 _atom_sites.fract_transf_matrix[1][2] 0.004349 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008698 _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] 0.011176 _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 GNP A 1 201 1 GNP GNP . D 4 MG A 1 202 5 MG MG . E 5 ZN A 1 203 8 ZN ZN . F 6 GOL B 1 201 2 GOL GOL . G 6 GOL B 1 202 3 GOL GOL . H 7 CL B 1 203 4 CL CL . I 5 ZN B 1 204 6 ZN ZN . J 5 ZN B 1 205 7 ZN ZN . K 8 HOH A 1 301 54 HOH HOH . K 8 HOH A 2 302 87 HOH HOH . K 8 HOH A 3 303 51 HOH HOH . K 8 HOH A 4 304 57 HOH HOH . K 8 HOH A 5 305 34 HOH HOH . K 8 HOH A 6 306 109 HOH HOH . K 8 HOH A 7 307 43 HOH HOH . K 8 HOH A 8 308 19 HOH HOH . K 8 HOH A 9 309 88 HOH HOH . K 8 HOH A 10 310 35 HOH HOH . K 8 HOH A 11 311 78 HOH HOH . K 8 HOH A 12 312 100 HOH HOH . K 8 HOH A 13 313 103 HOH HOH . K 8 HOH A 14 314 106 HOH HOH . K 8 HOH A 15 315 22 HOH HOH . K 8 HOH A 16 316 108 HOH HOH . K 8 HOH A 17 317 70 HOH HOH . K 8 HOH A 18 318 42 HOH HOH . K 8 HOH A 19 319 37 HOH HOH . K 8 HOH A 20 320 21 HOH HOH . K 8 HOH A 21 321 41 HOH HOH . K 8 HOH A 22 322 101 HOH HOH . K 8 HOH A 23 323 18 HOH HOH . K 8 HOH A 24 324 64 HOH HOH . K 8 HOH A 25 325 13 HOH HOH . K 8 HOH A 26 326 107 HOH HOH . K 8 HOH A 27 327 36 HOH HOH . K 8 HOH A 28 328 28 HOH HOH . K 8 HOH A 29 329 102 HOH HOH . K 8 HOH A 30 330 12 HOH HOH . K 8 HOH A 31 331 25 HOH HOH . K 8 HOH A 32 332 74 HOH HOH . K 8 HOH A 33 333 26 HOH HOH . K 8 HOH A 34 334 27 HOH HOH . K 8 HOH A 35 335 104 HOH HOH . K 8 HOH A 36 336 66 HOH HOH . K 8 HOH A 37 337 71 HOH HOH . K 8 HOH A 38 338 77 HOH HOH . K 8 HOH A 39 339 67 HOH HOH . K 8 HOH A 40 340 60 HOH HOH . K 8 HOH A 41 341 105 HOH HOH . K 8 HOH A 42 342 52 HOH HOH . K 8 HOH A 43 343 58 HOH HOH . K 8 HOH A 44 344 72 HOH HOH . K 8 HOH A 45 345 89 HOH HOH . K 8 HOH A 46 346 96 HOH HOH . L 8 HOH B 1 301 46 HOH HOH . L 8 HOH B 2 302 68 HOH HOH . L 8 HOH B 3 303 17 HOH HOH . L 8 HOH B 4 304 24 HOH HOH . L 8 HOH B 5 305 50 HOH HOH . L 8 HOH B 6 306 9 HOH HOH . L 8 HOH B 7 307 7 HOH HOH . L 8 HOH B 8 308 32 HOH HOH . L 8 HOH B 9 309 94 HOH HOH . L 8 HOH B 10 310 98 HOH HOH . L 8 HOH B 11 311 86 HOH HOH . L 8 HOH B 12 312 63 HOH HOH . L 8 HOH B 13 313 20 HOH HOH . L 8 HOH B 14 314 49 HOH HOH . L 8 HOH B 15 315 40 HOH HOH . L 8 HOH B 16 316 38 HOH HOH . L 8 HOH B 17 317 23 HOH HOH . L 8 HOH B 18 318 80 HOH HOH . L 8 HOH B 19 319 73 HOH HOH . L 8 HOH B 20 320 61 HOH HOH . L 8 HOH B 21 321 83 HOH HOH . L 8 HOH B 22 322 16 HOH HOH . L 8 HOH B 23 323 59 HOH HOH . L 8 HOH B 24 324 6 HOH HOH . L 8 HOH B 25 325 81 HOH HOH . L 8 HOH B 26 326 2 HOH HOH . L 8 HOH B 27 327 95 HOH HOH . L 8 HOH B 28 328 113 HOH HOH . L 8 HOH B 29 329 29 HOH HOH . L 8 HOH B 30 330 15 HOH HOH . L 8 HOH B 31 331 30 HOH HOH . L 8 HOH B 32 332 5 HOH HOH . L 8 HOH B 33 333 82 HOH HOH . L 8 HOH B 34 334 56 HOH HOH . L 8 HOH B 35 335 33 HOH HOH . L 8 HOH B 36 336 1 HOH HOH . L 8 HOH B 37 337 90 HOH HOH . L 8 HOH B 38 338 3 HOH HOH . L 8 HOH B 39 339 53 HOH HOH . L 8 HOH B 40 340 4 HOH HOH . L 8 HOH B 41 341 45 HOH HOH . L 8 HOH B 42 342 55 HOH HOH . L 8 HOH B 43 343 62 HOH HOH . L 8 HOH B 44 344 85 HOH HOH . L 8 HOH B 45 345 84 HOH HOH . L 8 HOH B 46 346 44 HOH HOH . L 8 HOH B 47 347 14 HOH HOH . L 8 HOH B 48 348 31 HOH HOH . L 8 HOH B 49 349 47 HOH HOH . L 8 HOH B 50 350 11 HOH HOH . L 8 HOH B 51 351 110 HOH HOH . L 8 HOH B 52 352 8 HOH HOH . L 8 HOH B 53 353 65 HOH HOH . L 8 HOH B 54 354 111 HOH HOH . L 8 HOH B 55 355 10 HOH HOH . L 8 HOH B 56 356 112 HOH HOH . L 8 HOH B 57 357 79 HOH HOH . L 8 HOH B 58 358 75 HOH HOH . L 8 HOH B 59 359 39 HOH HOH . L 8 HOH B 60 360 97 HOH HOH . L 8 HOH B 61 361 99 HOH HOH . L 8 HOH B 62 362 92 HOH HOH . L 8 HOH B 63 363 91 HOH HOH . L 8 HOH B 64 364 48 HOH HOH . L 8 HOH B 65 365 93 HOH HOH . L 8 HOH B 66 366 69 HOH HOH . L 8 HOH B 67 367 76 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 . . . C 3 47.169 41.647 10.863 0.17 48.37 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . C 3 47.27 40.132 10.826 1 50.17 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . C 3 46.938 42.07 12.312 1 48.08 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . C 3 48.558 42.236 10.491 0.27 56.71 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . C 3 46.003 42.33 9.765 1 50.13 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . C 3 44.374 42.515 10.054 1 46.17 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . C 3 44.096 42.672 11.528 1 44.23 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . C 3 43.626 41.317 9.493 1 46.99 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . C 3 43.751 43.818 9.274 1 47.38 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . C 3 43.235 45.169 9.951 1 48.19 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . C 3 44.4 45.752 10.751 1 49.75 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . C 3 41.976 44.98 10.722 1 49.67 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . C 3 42.964 46.081 8.702 1 52.74 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . C 3 43.963 46.261 7.676 1 51.82 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . C 3 43.601 47.44 6.795 1 58.43 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . C 3 42.386 47.16 6.054 1 49.73 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . C 3 43.346 48.759 7.526 1 61.77 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . C 3 43.772 49.85 6.715 1 61.49 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . C 3 41.828 48.74 7.709 1 53.43 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . C 3 41.252 50.026 7.865 1 56.5 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . C 3 41.397 48.125 6.377 1 53.29 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . C 3 40.081 47.463 6.421 1 48.47 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . C 3 39.681 46.49 7.293 1 48.42 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . C 3 38.449 46.086 7.092 1 47.32 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . C 3 38.007 46.849 6.031 1 49.68 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . C 3 36.736 46.868 5.345 1 53.18 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . C 3 35.746 46.165 5.587 1 48.26 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . C 3 36.722 47.795 4.315 1 53.74 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . C 3 37.772 48.606 3.97 1 53.78 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . C 3 37.579 49.435 2.942 1 56.64 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . C 3 38.95 48.596 4.595 1 48.36 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . C 3 39 47.703 5.602 1 50.35 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 32 #