data_5DGK # _model_server_result.job_id PPShom0Ogvam4jXr1zoqrA _model_server_result.datetime_utc '2025-08-31 16:29:42' _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 5dgk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 5DGK # _exptl.entry_id 5DGK _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 120 _cell.entry_id 5DGK _cell.length_a 110.14 _cell.length_b 110.14 _cell.length_c 302.755 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DGK _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 55.07 95.384038 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -55.07 95.384038 0 # 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 covale ? covale1 A C ARG 35 A ARG 35 1_555 A N MSE 36 A MSE 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C MSE 36 A MSE 36 1_555 A N ALA 37 A ALA 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C LEU 102 A LEU 102 1_555 A N MSE 103 A MSE 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 103 A MSE 103 1_555 A N ARG 104 A ARG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C ASN 165 A ASN 165 1_555 A N MSE 166 A MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C MSE 166 A MSE 166 1_555 A N TYR 167 A TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C ARG 395 A ARG 395 1_555 A N MSE 396 A MSE 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C MSE 396 A MSE 396 1_555 A N PHE 397 A PHE 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 A C ASN 467 A ASN 467 1_555 A N MSE 468 A MSE 468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 A C MSE 468 A MSE 468 1_555 A N PHE 469 A PHE 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale11 A C GLN 493 A GLN 493 1_555 A N MSE 494 A MSE 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 A C MSE 494 A MSE 494 1_555 A N LEU 495 A LEU 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 B C ARG 35 B ARG 35 1_555 B N MSE 36 B MSE 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 B C MSE 36 B MSE 36 1_555 B N ALA 37 B ALA 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 B C LEU 102 B LEU 102 1_555 B N MSE 103 B MSE 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale16 B C MSE 103 B MSE 103 1_555 B N ARG 104 B ARG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 B C ASN 165 B ASN 165 1_555 B N MSE 166 B MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale18 B C MSE 166 B MSE 166 1_555 B N TYR 167 B TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale19 B C ARG 395 B ARG 395 1_555 B N MSE 396 B MSE 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale20 B C MSE 396 B MSE 396 1_555 B N PHE 397 B PHE 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale21 B C ASN 467 B ASN 467 1_555 B N MSE 468 B MSE 468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale22 B C MSE 468 B MSE 468 1_555 B N PHE 469 B PHE 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale23 B C GLN 493 B GLN 493 1_555 B N MSE 494 B MSE 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale24 B C MSE 494 B MSE 494 1_555 B N LEU 495 B LEU 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OG SER 217 A SER 217 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 C O1G ANP . A ANP 701 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc3 C O1B ANP . A ANP 701 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc4 D MG MG . A MG 702 1_555 G O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc5 D MG MG . A MG 702 1_555 G O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc6 D MG MG . A MG 702 1_555 G O HOH . A HOH 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc7 B OG SER 217 B SER 217 1_555 F MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc8 E O1G ANP . B ANP 701 1_555 F MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc9 E O1B ANP . B ANP 701 1_555 F MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc10 F MG MG . B MG 702 1_555 H O HOH . B HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc11 F MG MG . B MG 702 1_555 H O HOH . B HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc12 F MG MG . B MG 702 1_555 H O HOH . B HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? # _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 5DGK _atom_sites.fract_transf_matrix[1][1] 0.009079 _atom_sites.fract_transf_matrix[1][2] 0.005242 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010484 _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] 0.003303 _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 1 701 2 ANP ANP . D 3 MG A 1 702 3 MG MG . E 2 ANP B 1 701 4 ANP ANP . F 3 MG B 1 702 5 MG MG . G 4 HOH A 1 801 5 HOH HOH . G 4 HOH A 2 802 4 HOH HOH . G 4 HOH A 3 803 7 HOH HOH . G 4 HOH A 4 804 6 HOH HOH . G 4 HOH A 5 805 5 HOH HOH . G 4 HOH A 6 806 2 HOH HOH . G 4 HOH A 7 807 1 HOH HOH . H 4 HOH B 1 801 6 HOH HOH . H 4 HOH B 2 802 13 HOH HOH . H 4 HOH B 3 803 7 HOH HOH . H 4 HOH B 4 804 8 HOH HOH . H 4 HOH B 5 805 6 HOH HOH . H 4 HOH B 6 806 14 HOH HOH . H 4 HOH B 7 807 4 HOH HOH . H 4 HOH B 8 808 8 HOH HOH . H 4 HOH B 9 809 3 HOH HOH . H 4 HOH B 10 810 12 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 ANP . . . E 2 11.924 33.3 195.583 1 16.7 ? PG ANP 701 B 1 HETATM 2 O O1G ANP . . . E 2 11.431 33.855 194.185 1 19.46 ? O1G ANP 701 B 1 HETATM 3 O O2G ANP . . . E 2 13.061 34.24 196.144 1 16.7 ? O2G ANP 701 B 1 HETATM 4 O O3G ANP . . . E 2 10.781 33.296 196.549 1 24.62 ? O3G ANP 701 B 1 HETATM 5 P PB ANP . . . E 2 11.317 30.638 194.99 1 16.7 ? PB ANP 701 B 1 HETATM 6 O O1B ANP . . . E 2 10.607 31.11 193.687 1 19.39 ? O1B ANP 701 B 1 HETATM 7 O O2B ANP . . . E 2 10.327 30.552 196.106 1 16.7 ? O2B ANP 701 B 1 HETATM 8 N N3B ANP . . . E 2 12.532 31.729 195.382 1 16.7 ? N3B ANP 701 B 1 HETATM 9 P PA ANP . . . E 2 12.549 28.841 193.355 1 16.7 ? PA ANP 701 B 1 HETATM 10 O O1A ANP . . . E 2 12.682 30.027 192.479 1 16.7 ? O1A ANP 701 B 1 HETATM 11 O O2A ANP . . . E 2 11.672 27.742 192.755 1 16.7 ? O2A ANP 701 B 1 HETATM 12 O O3A ANP . . . E 2 11.909 29.218 194.755 1 19.8 ? O3A ANP 701 B 1 HETATM 13 O O5' ANP . . . E 2 13.981 28.284 193.715 1 16.7 ? O5' ANP 701 B 1 HETATM 14 C C5' ANP . . . E 2 15.197 28.977 193.379 1 22.2 ? C5' ANP 701 B 1 HETATM 15 C C4' ANP . . . E 2 16.33 28.336 194.14 1 22.98 ? C4' ANP 701 B 1 HETATM 16 O O4' ANP . . . E 2 15.927 28.094 195.504 1 22.11 ? O4' ANP 701 B 1 HETATM 17 C C3' ANP . . . E 2 16.776 26.974 193.624 1 22.77 ? C3' ANP 701 B 1 HETATM 18 O O3' ANP . . . E 2 17.68 27.103 192.533 1 16.7 ? O3' ANP 701 B 1 HETATM 19 C C2' ANP . . . E 2 17.43 26.361 194.864 1 30.46 ? C2' ANP 701 B 1 HETATM 20 O O2' ANP . . . E 2 18.783 26.776 195.016 1 29.7 ? O2' ANP 701 B 1 HETATM 21 C C1' ANP . . . E 2 16.559 26.923 195.996 1 25.89 ? C1' ANP 701 B 1 HETATM 22 N N9 ANP . . . E 2 15.526 26.002 196.458 1 18.67 ? N9 ANP 701 B 1 HETATM 23 C C8 ANP . . . E 2 14.339 25.711 195.839 1 16.7 ? C8 ANP 701 B 1 HETATM 24 N N7 ANP . . . E 2 13.596 24.842 196.48 1 16.7 ? N7 ANP 701 B 1 HETATM 25 C C5 ANP . . . E 2 14.352 24.535 197.603 1 16.7 ? C5 ANP 701 B 1 HETATM 26 C C6 ANP . . . E 2 14.122 23.668 198.69 1 16.7 ? C6 ANP 701 B 1 HETATM 27 N N6 ANP . . . E 2 13.023 22.923 198.828 1 16.7 ? N6 ANP 701 B 1 HETATM 28 N N1 ANP . . . E 2 15.078 23.594 199.644 1 16.7 ? N1 ANP 701 B 1 HETATM 29 C C2 ANP . . . E 2 16.18 24.337 199.51 1 16.7 ? C2 ANP 701 B 1 HETATM 30 N N3 ANP . . . E 2 16.505 25.186 198.531 1 18.31 ? N3 ANP 701 B 1 HETATM 31 C C4 ANP . . . E 2 15.541 25.239 197.602 1 16.7 ? C4 ANP 701 B 1 HETATM 32 H HNB1 ANP . . . E 2 13.162 31.729 194.728 1 20.04 ? HNB1 ANP 701 B 1 HETATM 33 H "H5'1" ANP . . . E 2 15.12 29.915 193.626 1 26.64 ? "H5'1" ANP 701 B 1 HETATM 34 H "H5'2" ANP . . . E 2 15.363 28.903 192.416 1 26.64 ? "H5'2" ANP 701 B 1 HETATM 35 H H4' ANP . . . E 2 17.106 28.932 194.17 1 27.58 ? H4' ANP 701 B 1 HETATM 36 H H3' ANP . . . E 2 16.002 26.464 193.376 1 27.32 ? H3' ANP 701 B 1 HETATM 37 H H2' ANP . . . E 2 17.347 25.4 194.85 1 36.55 ? H2' ANP 701 B 1 HETATM 38 H HO2' ANP . . . E 2 19.287 26.074 195.22 1 35.64 ? HO2' ANP 701 B 1 HETATM 39 H H1' ANP . . . E 2 17.146 27.158 196.732 1 31.07 ? H1' ANP 701 B 1 HETATM 40 H H8 ANP . . . E 2 14.074 26.111 195.012 1 20.04 ? H8 ANP 701 B 1 HETATM 41 H HN61 ANP . . . E 2 12.985 22.08 198.452 1 20.04 ? HN61 ANP 701 B 1 HETATM 42 H HN62 ANP . . . E 2 12.307 23.247 199.295 1 20.04 ? HN62 ANP 701 B 1 HETATM 43 H H2 ANP . . . E 2 16.835 24.247 200.221 1 20.04 ? H2 ANP 701 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 69 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 491 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #