data_4X9L # _model_server_result.job_id kNR0E6KpHlElSZmXm4JeCg _model_server_result.datetime_utc '2024-10-20 05:52:52' _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 4x9l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4X9L # _exptl.entry_id 4X9L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _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 90 _cell.entry_id 4X9L _cell.length_a 116.87 _cell.length_b 116.87 _cell.length_c 105.34 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X9L _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 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 _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 # _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 4X9L _atom_sites.fract_transf_matrix[1][1] 0.008557 _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] 0.008557 _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] 0.009493 _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 ACP A 1 301 1 ACP ACP . C 3 PG4 A 1 302 1 PG4 PG4 . D 4 HOH A 1 401 1 HOH HOH . D 4 HOH A 2 402 7 HOH HOH . D 4 HOH A 3 403 2 HOH HOH . D 4 HOH A 4 404 3 HOH HOH . D 4 HOH A 5 405 4 HOH HOH . D 4 HOH A 6 406 5 HOH HOH . D 4 HOH A 7 407 8 HOH HOH . D 4 HOH A 8 408 9 HOH HOH . D 4 HOH A 9 409 10 HOH HOH . D 4 HOH A 10 410 11 HOH HOH . D 4 HOH A 11 411 12 HOH HOH . D 4 HOH A 12 412 13 HOH HOH . D 4 HOH A 13 413 14 HOH HOH . D 4 HOH A 14 414 15 HOH HOH . D 4 HOH A 15 415 16 HOH HOH . D 4 HOH A 16 416 17 HOH HOH . D 4 HOH A 17 417 18 HOH HOH . D 4 HOH A 18 418 19 HOH HOH . D 4 HOH A 19 419 20 HOH HOH . D 4 HOH A 20 420 21 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 . . . B 2 21.399 12.16 6.588 1 135.85 ? PG ACP 301 A 1 HETATM 2 O O1G ACP . . . B 2 22.347 11.684 5.51 1 127.74 ? O1G ACP 301 A 1 HETATM 3 O O2G ACP . . . B 2 20.093 11.371 6.691 1 91.69 ? O2G ACP 301 A 1 HETATM 4 O O3G ACP . . . B 2 22.137 12.473 7.869 1 114.6 ? O3G ACP 301 A 1 HETATM 5 P PB ACP . . . B 2 20.322 14.795 7.495 1 159.24 ? PB ACP 301 A 1 HETATM 6 O O1B ACP . . . B 2 19.703 16.012 6.842 1 136.67 ? O1B ACP 301 A 1 HETATM 7 O O2B ACP . . . B 2 21.471 15.053 8.449 1 114.62 ? O2B ACP 301 A 1 HETATM 8 C C3B ACP . . . B 2 20.907 13.824 6.072 1 134.01 ? C3B ACP 301 A 1 HETATM 9 P PA ACP . . . B 2 19.093 13.465 9.798 1 108.4 ? PA ACP 301 A 1 HETATM 10 O O1A ACP . . . B 2 18.04 12.394 10.011 1 120.79 ? O1A ACP 301 A 1 HETATM 11 O O2A ACP . . . B 2 20.534 13.133 10.122 1 84.7 ? O2A ACP 301 A 1 HETATM 12 O O3A ACP . . . B 2 19.12 13.967 8.245 1 146.34 ? O3A ACP 301 A 1 HETATM 13 O O5' ACP . . . B 2 18.558 14.737 10.649 1 98.75 ? O5' ACP 301 A 1 HETATM 14 C C5' ACP . . . B 2 17.498 15.566 10.16 1 98.33 ? C5' ACP 301 A 1 HETATM 15 C C4' ACP . . . B 2 17.771 17.082 10.251 1 100.88 ? C4' ACP 301 A 1 HETATM 16 O O4' ACP . . . B 2 18.222 17.53 11.54 1 87.62 ? O4' ACP 301 A 1 HETATM 17 C C3' ACP . . . B 2 18.804 17.666 9.288 1 103.31 ? C3' ACP 301 A 1 HETATM 18 O O3' ACP . . . B 2 18.319 17.824 7.955 1 104.69 ? O3' ACP 301 A 1 HETATM 19 C C2' ACP . . . B 2 19.035 19.02 9.902 1 98.15 ? C2' ACP 301 A 1 HETATM 20 O O2' ACP . . . B 2 17.909 19.86 9.625 1 87.09 ? O2' ACP 301 A 1 HETATM 21 C C1' ACP . . . B 2 19.037 18.717 11.385 1 91.11 ? C1' ACP 301 A 1 HETATM 22 N N9 ACP . . . B 2 20.456 18.54 11.828 1 89.64 ? N9 ACP 301 A 1 HETATM 23 C C8 ACP . . . B 2 21.126 17.373 11.937 1 83.47 ? C8 ACP 301 A 1 HETATM 24 N N7 ACP . . . B 2 22.398 17.57 12.38 1 84.17 ? N7 ACP 301 A 1 HETATM 25 C C5 ACP . . . B 2 22.57 18.897 12.567 1 83.22 ? C5 ACP 301 A 1 HETATM 26 C C6 ACP . . . B 2 23.673 19.79 13.022 1 70.65 ? C6 ACP 301 A 1 HETATM 27 N N6 ACP . . . B 2 24.889 19.296 13.378 1 74.04 ? N6 ACP 301 A 1 HETATM 28 N N1 ACP . . . B 2 23.423 21.122 13.071 1 69.83 ? N1 ACP 301 A 1 HETATM 29 C C2 ACP . . . B 2 22.224 21.638 12.727 1 76.64 ? C2 ACP 301 A 1 HETATM 30 N N3 ACP . . . B 2 21.184 20.888 12.309 1 87.37 ? N3 ACP 301 A 1 HETATM 31 C C4 ACP . . . B 2 21.285 19.532 12.211 1 93.24 ? C4 ACP 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #