data_4KH4 # _model_server_result.job_id EfYBA0TA-fG4Izm7Y865lw _model_server_result.datetime_utc '2024-11-26 13:08:50' _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 4kh4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":700}' # _entry.id 4KH4 # _exptl.entry_id 4KH4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 4KH4 _cell.length_a 74.156 _cell.length_b 148.267 _cell.length_c 242.176 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KH4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -121.088 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 disulf ? disulf1 A SG CYS 35 A CYS 59 1_555 A SG CYS 64 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 317 A CYS 341 1_555 A SG CYS 328 A CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 332 A CYS 356 1_555 A SG CYS 421 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 341 A CYS 365 1_555 A SG CYS 409 A CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 372 A CYS 396 1_555 A SG CYS 389 A CYS 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 A SG CYS 502 A CYS 526 1_555 A SG CYS 534 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 35 B CYS 59 1_555 B SG CYS 64 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 317 B CYS 341 1_555 B SG CYS 328 B CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 332 B CYS 356 1_555 B SG CYS 421 B CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 B SG CYS 341 B CYS 365 1_555 B SG CYS 409 B CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 372 B CYS 396 1_555 B SG CYS 389 B CYS 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 B SG CYS 502 B CYS 526 1_555 B SG CYS 534 B CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 C O2G ANP . A ANP 700 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc2 C O1B ANP . A ANP 700 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc3 E O1B ANP . B ANP 700 1_555 F MG MG . B MG 701 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc4 E O1B ANP . B ANP 700 1_555 F MG MG . B MG 701 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc5 E O1G ANP . B ANP 700 1_555 F MG MG . B MG 701 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc6 E O1G ANP . B ANP 700 1_555 F MG MG . B MG 701 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc7 E O3A ANP . B ANP 700 1_555 F MG MG . B MG 701 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.988 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 4KH4 _atom_sites.fract_transf_matrix[1][1] 0.013485 _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] 0.006745 _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] 0.004129 _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 2 ANP A 1 700 700 ANP ANP . D 3 MG A 1 701 701 MG MG . E 2 ANP B 1 700 700 ANP ANP . F 3 MG B 1 701 701 MG MG . # 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 ANP . A . E 2 -5.967 10.884 -27.113 0.8 69.61 ? PG ANP 700 B 1 HETATM 2 P PG ANP . B . E 2 -5.98 11.004 -27.047 0 71.5 ? PG ANP 700 B 1 HETATM 3 O O1G ANP . A . E 2 -5.076 10.562 -28.275 0.8 69.88 ? O1G ANP 700 B 1 HETATM 4 O O1G ANP . B . E 2 -5.108 10.472 -28.141 0 71.5 ? O1G ANP 700 B 1 HETATM 5 O O2G ANP . A . E 2 -7.318 11.294 -27.615 0.8 69.6 ? O2G ANP 700 B 1 HETATM 6 O O2G ANP . B . E 2 -7.325 11.353 -27.606 0 71.5 ? O2G ANP 700 B 1 HETATM 7 O O3G ANP . A . E 2 -6.099 9.677 -26.241 0.8 69.65 ? O3G ANP 700 B 1 HETATM 8 O O3G ANP . B . E 2 -6.131 9.965 -25.979 0 71.5 ? O3G ANP 700 B 1 HETATM 9 P PB ANP . A . E 2 -4.415 13.402 -26.74 0.8 68.7 ? PB ANP 700 B 1 HETATM 10 P PB ANP . B . E 2 -4.146 13.356 -27.031 0 71.5 ? PB ANP 700 B 1 HETATM 11 O O1B ANP . A . E 2 -4.371 13.429 -28.215 0.8 69.13 ? O1B ANP 700 B 1 HETATM 12 O O1B ANP . B . E 2 -4.204 13.307 -28.507 0 71.5 ? O1B ANP 700 B 1 HETATM 13 O O2B ANP . A . E 2 -5.07 14.739 -26.203 0.8 68.03 ? O2B ANP 700 B 1 HETATM 14 O O2B ANP . B . E 2 -4.422 14.838 -26.543 0 71.5 ? O2B ANP 700 B 1 HETATM 15 N N3B ANP . A . E 2 -5.311 12.115 -26.24 0.8 69.21 ? N3B ANP 700 B 1 HETATM 16 N N3B ANP . B . E 2 -5.289 12.353 -26.403 0 71.5 ? N3B ANP 700 B 1 HETATM 17 P PA ANP . A . E 2 -1.776 14.329 -26.037 0.8 70.64 ? PA ANP 700 B 1 HETATM 18 P PA ANP . B . E 2 -1.361 13.664 -26.205 0 71.5 ? PA ANP 700 B 1 HETATM 19 O O1A ANP . A . E 2 -0.535 13.79 -26.645 0.8 71.15 ? O1A ANP 700 B 1 HETATM 20 O O1A ANP . B . E 2 -0.2 12.804 -26.538 0 71.5 ? O1A ANP 700 B 1 HETATM 21 O O2A ANP . A . E 2 -2.171 15.627 -26.749 0.8 71.2 ? O2A ANP 700 B 1 HETATM 22 O O2A ANP . B . E 2 -1.292 14.952 -27.03 0 71.5 ? O2A ANP 700 B 1 HETATM 23 O O3A ANP . A . E 2 -2.942 13.269 -26.181 0.8 69.2 ? O3A ANP 700 B 1 HETATM 24 O O3A ANP . B . E 2 -2.705 12.889 -26.542 0 71.5 ? O3A ANP 700 B 1 HETATM 25 O O5' ANP . A . E 2 -1.524 14.628 -24.479 0.8 70.64 ? O5' ANP 700 B 1 HETATM 26 O O5' ANP . B . E 2 -1.329 14.022 -24.629 0 71.5 ? O5' ANP 700 B 1 HETATM 27 C C5' ANP . A . E 2 -2.471 15.388 -23.704 0.8 70.86 ? C5' ANP 700 B 1 HETATM 28 C C5' ANP . B . E 2 -2.159 15.053 -24.056 0 71.5 ? C5' ANP 700 B 1 HETATM 29 C C4' ANP . A . E 2 -1.975 15.5 -22.284 0.8 71.01 ? C4' ANP 700 B 1 HETATM 30 C C4' ANP . B . E 2 -1.77 15.279 -22.615 0 71.5 ? C4' ANP 700 B 1 HETATM 31 O O4' ANP . A . E 2 -0.605 15.966 -22.291 0.8 71.24 ? O4' ANP 700 B 1 HETATM 32 O O4' ANP . B . E 2 -0.329 15.357 -22.509 0 71.5 ? O4' ANP 700 B 1 HETATM 33 C C3' ANP . A . E 2 -2.767 16.479 -21.418 0.8 70.78 ? C3' ANP 700 B 1 HETATM 34 C C3' ANP . B . E 2 -2.323 16.569 -22.007 0 71.5 ? C3' ANP 700 B 1 HETATM 35 O O3' ANP . A . E 2 -3.749 15.805 -20.639 0.8 70.28 ? O3' ANP 700 B 1 HETATM 36 O O3' ANP . B . E 2 -3.502 16.316 -21.251 0 71.5 ? O3' ANP 700 B 1 HETATM 37 C C2' ANP . A . E 2 -1.685 17.154 -20.567 0.8 71.24 ? C2' ANP 700 B 1 HETATM 38 C C2' ANP . B . E 2 -1.165 17.08 -21.142 0 71.5 ? C2' ANP 700 B 1 HETATM 39 O O2' ANP . A . E 2 -1.396 16.437 -19.372 0.8 71.42 ? O2' ANP 700 B 1 HETATM 40 O O2' ANP . B . E 2 -1.175 16.548 -19.822 0 71.5 ? O2' ANP 700 B 1 HETATM 41 C C1' ANP . A . E 2 -0.481 17.137 -21.511 0.8 71.15 ? C1' ANP 700 B 1 HETATM 42 C C1' ANP . B . E 2 0.054 16.584 -21.922 0 71.5 ? C1' ANP 700 B 1 HETATM 43 N N9 ANP . A . E 2 -0.34 18.288 -22.408 0.8 70.89 ? N9 ANP 700 B 1 HETATM 44 N N9 ANP . B . E 2 0.588 17.457 -22.974 0 71.5 ? N9 ANP 700 B 1 HETATM 45 C C8 ANP . A . E 2 -1.041 19.467 -22.373 0.8 70.76 ? C8 ANP 700 B 1 HETATM 46 C C8 ANP . B . E 2 1.545 17.09 -23.885 0 71.5 ? C8 ANP 700 B 1 HETATM 47 N N7 ANP . A . E 2 -0.65 20.35 -23.257 0.8 70.56 ? N7 ANP 700 B 1 HETATM 48 N N7 ANP . B . E 2 1.891 18.044 -24.714 0 71.5 ? N7 ANP 700 B 1 HETATM 49 C C5 ANP . A . E 2 0.383 19.711 -23.926 0.8 70.46 ? C5 ANP 700 B 1 HETATM 50 C C5 ANP . B . E 2 1.106 19.118 -24.326 0 71.5 ? C5 ANP 700 B 1 HETATM 51 C C6 ANP . A . E 2 1.241 20.124 -24.967 0.8 70.19 ? C6 ANP 700 B 1 HETATM 52 C C6 ANP . B . E 2 1.001 20.441 -24.807 0 71.5 ? C6 ANP 700 B 1 HETATM 53 N N6 ANP . A . E 2 1.214 21.343 -25.509 0.8 69.81 ? N6 ANP 700 B 1 HETATM 54 N N6 ANP . B . E 2 1.732 20.923 -25.814 0 71.5 ? N6 ANP 700 B 1 HETATM 55 N N1 ANP . A . E 2 2.166 19.239 -25.408 0.8 70.58 ? N1 ANP 700 B 1 HETATM 56 N N1 ANP . B . E 2 0.117 21.264 -24.197 0 71.5 ? N1 ANP 700 B 1 HETATM 57 C C2 ANP . A . E 2 2.228 18.031 -24.836 0.8 70.59 ? C2 ANP 700 B 1 HETATM 58 C C2 ANP . B . E 2 -0.604 20.793 -23.173 0 71.5 ? C2 ANP 700 B 1 HETATM 59 N N3 ANP . A . E 2 1.485 17.536 -23.84 0.8 70.55 ? N3 ANP 700 B 1 HETATM 60 N N3 ANP . B . E 2 -0.586 19.571 -22.631 0 71.5 ? N3 ANP 700 B 1 HETATM 61 C C4 ANP . A . E 2 0.576 18.433 -23.423 0.8 70.73 ? C4 ANP 700 B 1 HETATM 62 C C4 ANP . B . E 2 0.295 18.773 -23.256 0 71.5 ? C4 ANP 700 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 62 #