data_4DSN # _model_server_result.job_id NdjlacNvjmtJfCRiNMVLXQ _model_server_result.datetime_utc '2024-10-15 16:17:41' _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 4dsn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4DSN # _exptl.entry_id 4DSN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC 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 4DSN _cell.length_a 78.638 _cell.length_b 78.638 _cell.length_c 77.353 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DSN _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 O GLY 11 A GLY 10 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc2 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc3 A OG1 THR 36 A THR 35 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc4 A O ALA 60 A ALA 59 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc5 A O GLY 61 A GLY 60 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc6 A OH TYR 97 A TYR 96 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc7 B O1G GCP . A GCP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc8 B O2B GCP . A GCP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc9 C MG MG . A MG 202 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc10 C MG MG . A MG 202 1_555 G O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc11 D MG MG . A MG 203 1_555 G O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc12 D MG MG . A MG 203 1_555 G O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? # _chem_comp.formula 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id GCP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC 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 GCP doub 92 n n PG O2G GCP sing 93 n n PG O3G GCP sing 94 n n PG C3B GCP sing 95 n n O2G HOG2 GCP sing 96 n n O3G HOG3 GCP sing 97 n n C3B PB GCP sing 98 n n C3B H3B1 GCP sing 99 n n C3B H3B2 GCP sing 100 n n PB O1B GCP doub 101 n n PB O2B GCP sing 102 n n PB O3A GCP sing 103 n n O2B HOB2 GCP sing 104 n n O3A PA GCP sing 105 n n PA O1A GCP doub 106 n n PA O2A GCP sing 107 n n PA O5' GCP sing 108 n n O2A HOA2 GCP sing 109 n n O5' C5' GCP sing 110 n n C5' C4' GCP sing 111 n n C5' "H5'2" GCP sing 112 n n C5' "H5'1" GCP sing 113 n n C4' O4' GCP sing 114 n n C4' C3' GCP sing 115 n n C4' H4' GCP sing 116 n n O4' C1' GCP sing 117 n n C3' O3' GCP sing 118 n n C3' C2' GCP sing 119 n n C3' H3' GCP sing 120 n n O3' HO3' GCP sing 121 n n C2' O2' GCP sing 122 n n C2' C1' GCP sing 123 n n C2' H2' GCP sing 124 n n O2' HO2' GCP sing 125 n n C1' N9 GCP sing 126 n n C1' H1' GCP sing 127 n n N9 C8 GCP sing 128 n y N9 C4 GCP sing 129 n y C8 N7 GCP doub 130 n y C8 H8 GCP sing 131 n n N7 C5 GCP sing 132 n y C5 C6 GCP sing 133 n y C5 C4 GCP doub 134 n y C6 O6 GCP doub 135 n n C6 N1 GCP sing 136 n y N1 C2 GCP sing 137 n y N1 HN1 GCP sing 138 n n C2 N2 GCP sing 139 n n C2 N3 GCP doub 140 n y N2 HN21 GCP sing 141 n n N2 HN22 GCP sing 142 n n N3 C4 GCP sing 143 n y # _atom_sites.entry_id 4DSN _atom_sites.fract_transf_matrix[1][1] 0.012716 _atom_sites.fract_transf_matrix[1][2] 0.007342 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014684 _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] 0.012928 _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 B 2 GCP A 1 201 1 GCP GCP . C 3 MG A 1 202 2 MG MG . D 3 MG A 1 203 3 MG MG . E 4 EDO A 1 204 5 EDO EDO . F 4 EDO A 1 205 6 EDO EDO . G 5 HOH A 1 301 1 HOH HOH . G 5 HOH A 2 302 2 HOH HOH . G 5 HOH A 3 303 3 HOH HOH . G 5 HOH A 4 304 4 HOH HOH . G 5 HOH A 5 305 5 HOH HOH . G 5 HOH A 6 306 6 HOH HOH . G 5 HOH A 7 307 7 HOH HOH . G 5 HOH A 8 308 8 HOH HOH . G 5 HOH A 9 309 9 HOH HOH . G 5 HOH A 10 310 10 HOH HOH . G 5 HOH A 11 311 11 HOH HOH . G 5 HOH A 12 312 12 HOH HOH . G 5 HOH A 13 313 13 HOH HOH . G 5 HOH A 14 314 14 HOH HOH . G 5 HOH A 15 315 15 HOH HOH . G 5 HOH A 16 316 16 HOH HOH . G 5 HOH A 17 317 17 HOH HOH . G 5 HOH A 18 318 18 HOH HOH . G 5 HOH A 19 319 19 HOH HOH . G 5 HOH A 20 320 20 HOH HOH . G 5 HOH A 21 321 21 HOH HOH . G 5 HOH A 22 322 22 HOH HOH . G 5 HOH A 23 323 23 HOH HOH . G 5 HOH A 24 324 24 HOH HOH . G 5 HOH A 25 325 25 HOH HOH . G 5 HOH A 26 326 26 HOH HOH . G 5 HOH A 27 327 27 HOH HOH . G 5 HOH A 28 328 28 HOH HOH . G 5 HOH A 29 329 29 HOH HOH . G 5 HOH A 30 330 30 HOH HOH . G 5 HOH A 31 331 31 HOH HOH . G 5 HOH A 32 332 32 HOH HOH . G 5 HOH A 33 333 33 HOH HOH . G 5 HOH A 34 334 34 HOH HOH . G 5 HOH A 35 335 35 HOH HOH . G 5 HOH A 36 336 36 HOH HOH . G 5 HOH A 37 337 37 HOH HOH . G 5 HOH A 38 338 38 HOH HOH . G 5 HOH A 39 339 39 HOH HOH . G 5 HOH A 40 340 40 HOH HOH . G 5 HOH A 41 341 41 HOH HOH . G 5 HOH A 42 342 42 HOH HOH . G 5 HOH A 43 343 43 HOH HOH . G 5 HOH A 44 344 44 HOH HOH . G 5 HOH A 45 345 45 HOH HOH . G 5 HOH A 46 346 46 HOH HOH . G 5 HOH A 47 347 47 HOH HOH . G 5 HOH A 48 348 48 HOH HOH . G 5 HOH A 49 349 49 HOH HOH . G 5 HOH A 50 350 50 HOH HOH . G 5 HOH A 51 351 52 HOH HOH . G 5 HOH A 52 352 53 HOH HOH . G 5 HOH A 53 353 54 HOH HOH . G 5 HOH A 54 354 55 HOH HOH . G 5 HOH A 55 355 56 HOH HOH . G 5 HOH A 56 356 57 HOH HOH . G 5 HOH A 57 357 58 HOH HOH . G 5 HOH A 58 358 59 HOH HOH . G 5 HOH A 59 359 60 HOH HOH . G 5 HOH A 60 360 61 HOH HOH . G 5 HOH A 61 361 62 HOH HOH . G 5 HOH A 62 362 63 HOH HOH . G 5 HOH A 63 363 64 HOH HOH . G 5 HOH A 64 364 65 HOH HOH . G 5 HOH A 65 365 66 HOH HOH . G 5 HOH A 66 366 67 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 GCP . . . B 2 14.71 0.621 6.599 1 34.45 ? PG GCP 201 A 1 HETATM 2 O O1G GCP . . . B 2 15.949 1.324 7.051 1 34.62 ? O1G GCP 201 A 1 HETATM 3 O O2G GCP . . . B 2 14.067 -0.13 7.737 1 37.6 ? O2G GCP 201 A 1 HETATM 4 O O3G GCP . . . B 2 13.778 1.54 5.843 1 35.45 ? O3G GCP 201 A 1 HETATM 5 C C3B GCP . . . B 2 15.22 -0.669 5.43 1 28.84 ? C3B GCP 201 A 1 HETATM 6 P PB GCP . . . B 2 16.107 -0.058 3.967 1 29.78 ? PB GCP 201 A 1 HETATM 7 O O1B GCP . . . B 2 15.257 0.836 3.107 1 31.03 ? O1B GCP 201 A 1 HETATM 8 O O2B GCP . . . B 2 17.464 0.461 4.328 1 29.58 ? O2B GCP 201 A 1 HETATM 9 O O3A GCP . . . B 2 16.387 -1.373 3.082 1 25.65 ? O3A GCP 201 A 1 HETATM 10 P PA GCP . . . B 2 17.638 -2.374 3.306 1 31.36 ? PA GCP 201 A 1 HETATM 11 O O1A GCP . . . B 2 18.859 -1.895 2.57 1 33.15 ? O1A GCP 201 A 1 HETATM 12 O O2A GCP . . . B 2 17.757 -2.711 4.765 1 33.8 ? O2A GCP 201 A 1 HETATM 13 O O5' GCP . . . B 2 17.057 -3.634 2.496 1 31.71 ? O5' GCP 201 A 1 HETATM 14 C C5' GCP . . . B 2 15.86 -4.308 2.893 1 32.14 ? C5' GCP 201 A 1 HETATM 15 C C4' GCP . . . B 2 15.792 -5.66 2.185 1 32.96 ? C4' GCP 201 A 1 HETATM 16 O O4' GCP . . . B 2 15.811 -5.49 0.76 1 32.08 ? O4' GCP 201 A 1 HETATM 17 C C3' GCP . . . B 2 17 -6.511 2.51 1 34.18 ? C3' GCP 201 A 1 HETATM 18 O O3' GCP . . . B 2 16.593 -7.884 2.49 1 35.42 ? O3' GCP 201 A 1 HETATM 19 C C2' GCP . . . B 2 17.942 -6.26 1.355 1 30.61 ? C2' GCP 201 A 1 HETATM 20 O O2' GCP . . . B 2 18.824 -7.361 1.131 1 32.38 ? O2' GCP 201 A 1 HETATM 21 C C1' GCP . . . B 2 16.974 -6.115 0.203 1 29.83 ? C1' GCP 201 A 1 HETATM 22 N N9 GCP . . . B 2 17.537 -5.282 -0.886 1 30.41 ? N9 GCP 201 A 1 HETATM 23 C C8 GCP . . . B 2 18.064 -4.044 -0.772 1 27.26 ? C8 GCP 201 A 1 HETATM 24 N N7 GCP . . . B 2 18.468 -3.587 -1.983 1 25.81 ? N7 GCP 201 A 1 HETATM 25 C C5 GCP . . . B 2 18.193 -4.544 -2.893 1 25.4 ? C5 GCP 201 A 1 HETATM 26 C C6 GCP . . . B 2 18.358 -4.71 -4.352 1 27.87 ? C6 GCP 201 A 1 HETATM 27 O O6 GCP . . . B 2 18.874 -3.806 -5.046 1 26.25 ? O6 GCP 201 A 1 HETATM 28 N N1 GCP . . . B 2 17.932 -5.854 -4.905 1 27.92 ? N1 GCP 201 A 1 HETATM 29 C C2 GCP . . . B 2 17.376 -6.845 -4.181 1 30.67 ? C2 GCP 201 A 1 HETATM 30 N N2 GCP . . . B 2 16.976 -7.97 -4.818 1 26.92 ? N2 GCP 201 A 1 HETATM 31 N N3 GCP . . . B 2 17.194 -6.764 -2.837 1 28.89 ? N3 GCP 201 A 1 HETATM 32 C C4 GCP . . . B 2 17.576 -5.654 -2.164 1 26.5 ? C4 GCP 201 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #