data_7Z67 # _model_server_result.job_id Lnh7EPKaOj-Rj6T6vQ85dA _model_server_result.datetime_utc '2025-03-13 17:52:27' _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 7z67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 7Z67 # _exptl.entry_id 7Z67 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE 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 7Z67 _cell.length_a 93.37 _cell.length_b 93.37 _cell.length_c 266.327 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Z67 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _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 4 _struct_asym.id D _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 C PHE 72 A PHE 88 1_555 A N MSE 73 A MSE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 73 A MSE 89 1_555 A N PRO 74 A PRO 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C ASN 80 A ASN 96 1_555 A N MSE 81 A MSE 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 81 A MSE 97 1_555 A N ASP 82 A ASP 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale5 A C PRO 203 A PRO 219 1_555 A N MSE 204 A MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 204 A MSE 220 1_555 A N TYR 205 A TYR 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 A C GLN 247 A GLN 263 1_555 A N MSE 248 A MSE 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C MSE 248 A MSE 264 1_555 A N LYS 249 A LYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale9 A C ARG 283 A ARG 299 1_555 A N MSE 284 A MSE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C MSE 284 A MSE 300 1_555 A N ARG 285 A ARG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 A C LEU 293 A LEU 309 1_555 A N MSE 294 A MSE 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 A C MSE 294 A MSE 310 1_555 A N PHE 295 A PHE 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 A C LEU 322 A LEU 338 1_555 A N MSE 323 A MSE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 A C MSE 323 A MSE 339 1_555 A N ALA 324 A ALA 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? metalc ? metalc1 A OH TYR 267 A TYR 283 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc2 B O3 CIT . A CIT 501 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.917 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 7Z67 _atom_sites.fract_transf_matrix[1][1] 0.01071 _atom_sites.fract_transf_matrix[1][2] 0.006183 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012367 _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] 0.003755 _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 CIT A 1 501 602 CIT CIT . C 3 EDO A 1 502 603 EDO EDO . D 4 ACP A 1 503 604 ACP ACP . E 5 MG A 1 504 1 MG MG . F 6 NA A 1 505 1 NA NA . G 7 HOH A 1 601 2 HOH HOH . G 7 HOH A 2 602 4 HOH HOH . G 7 HOH A 3 603 3 HOH HOH . G 7 HOH A 4 604 1 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 ACP . . . D 4 -29.262 19.54 -0.772 1 135.37 ? PG ACP 503 A 1 HETATM 2 O O1G ACP . . . D 4 -28.047 18.677 -0.648 1 91.45 ? O1G ACP 503 A 1 HETATM 3 O O2G ACP . . . D 4 -29.054 20.939 -0.148 1 131.22 ? O2G ACP 503 A 1 HETATM 4 O O3G ACP . . . D 4 -30.506 18.907 -0.109 1 122.08 ? O3G ACP 503 A 1 HETATM 5 P PB ACP . . . D 4 -31.119 20.906 -2.709 1 114.64 ? PB ACP 503 A 1 HETATM 6 O O1B ACP . . . D 4 -32.272 20.081 -3.225 1 79.13 ? O1B ACP 503 A 1 HETATM 7 O O2B ACP . . . D 4 -31.539 21.484 -1.323 1 121.39 ? O2B ACP 503 A 1 HETATM 8 C C3B ACP . . . D 4 -29.679 19.803 -2.499 1 106.93 ? C3B ACP 503 A 1 HETATM 9 P PA ACP . . . D 4 -29.355 22.488 -4.109 1 150.94 ? PA ACP 503 A 1 HETATM 10 O O1A ACP . . . D 4 -28.475 22.52 -2.921 1 127.11 ? O1A ACP 503 A 1 HETATM 11 O O2A ACP . . . D 4 -29.392 23.833 -4.833 1 109.64 ? O2A ACP 503 A 1 HETATM 12 O O3A ACP . . . D 4 -30.888 22.117 -3.765 1 120.35 ? O3A ACP 503 A 1 HETATM 13 O O5' ACP . . . D 4 -28.917 21.411 -5.179 1 126.43 ? O5' ACP 503 A 1 HETATM 14 C C5' ACP . . . D 4 -27.637 20.749 -5.095 1 122.72 ? C5' ACP 503 A 1 HETATM 15 C C4' ACP . . . D 4 -26.905 20.783 -6.417 1 126.67 ? C4' ACP 503 A 1 HETATM 16 O O4' ACP . . . D 4 -27.842 20.799 -7.516 1 136.98 ? O4' ACP 503 A 1 HETATM 17 C C3' ACP . . . D 4 -25.961 21.974 -6.62 1 122.13 ? C3' ACP 503 A 1 HETATM 18 O O3' ACP . . . D 4 -24.621 21.531 -6.806 1 93.11 ? O3' ACP 503 A 1 HETATM 19 C C2' ACP . . . D 4 -26.506 22.668 -7.878 1 123.96 ? C2' ACP 503 A 1 HETATM 20 O O2' ACP . . . D 4 -25.461 23.164 -8.706 1 117.42 ? O2' ACP 503 A 1 HETATM 21 C C1' ACP . . . D 4 -27.243 21.523 -8.564 1 128.65 ? C1' ACP 503 A 1 HETATM 22 N N9 ACP . . . D 4 -28.282 21.943 -9.499 1 124.66 ? N9 ACP 503 A 1 HETATM 23 C C8 ACP . . . D 4 -29.637 21.891 -9.305 1 108.15 ? C8 ACP 503 A 1 HETATM 24 N N7 ACP . . . D 4 -30.34 22.332 -10.32 1 109.3 ? N7 ACP 503 A 1 HETATM 25 C C5 ACP . . . D 4 -29.382 22.699 -11.249 1 119.66 ? C5 ACP 503 A 1 HETATM 26 C C6 ACP . . . D 4 -29.47 23.245 -12.547 1 112.85 ? C6 ACP 503 A 1 HETATM 27 N N6 ACP . . . D 4 -30.628 23.527 -13.155 1 100.77 ? N6 ACP 503 A 1 HETATM 28 N N1 ACP . . . D 4 -28.318 23.493 -13.207 1 104.97 ? N1 ACP 503 A 1 HETATM 29 C C2 ACP . . . D 4 -27.159 23.213 -12.605 1 104.74 ? C2 ACP 503 A 1 HETATM 30 N N3 ACP . . . D 4 -26.951 22.7 -11.39 1 130.66 ? N3 ACP 503 A 1 HETATM 31 C C4 ACP . . . D 4 -28.105 22.464 -10.76 1 132.07 ? C4 ACP 503 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 60 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 1333 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #