data_1KQM # _model_server_result.job_id QqHKW9R0DkPDLRMb6-ldtA _model_server_result.datetime_utc '2024-11-23 02:47:36' _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 1kqm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":999}' # _entry.id 1KQM # _exptl.entry_id 1KQM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 81.64 _cell.angle_beta 82.39 _cell.angle_gamma 87.43 _cell.entry_id 1KQM _cell.length_a 52.396 _cell.length_b 58.642 _cell.length_c 148.873 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KQM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I,J _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 5 _struct_asym.id E _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 ND2 ASN 237 A ASN 237 1_555 E O2A ANP . A ANP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? covale ? covale2 A OG SER 240 A SER 240 1_555 E O2G ANP . A ANP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc1 A OG1 THR 183 A THR 183 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc2 A OG SER 241 A SER 241 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc3 D MG MG . A MG 903 1_555 E O3G ANP . A ANP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc4 D MG MG . A MG 903 1_555 E O1A ANP . A ANP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.08 ? metalc ? metalc5 D MG MG . A MG 903 1_555 E O2B ANP . A ANP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc6 D MG MG . A MG 903 1_555 H O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc7 B OD1 ASP 28 B ASP 28 1_555 F MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? metalc ? metalc8 B OD2 ASP 30 B ASP 30 1_555 F MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc9 B OD2 ASP 32 B ASP 32 1_555 F MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc10 B OD1 ASP 32 B ASP 32 1_555 F MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc11 B O PHE 34 B PHE 34 1_555 F MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc12 B OD2 ASP 39 B ASP 39 1_555 F MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc13 F MG MG . B MG 502 1_555 I O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc14 C OD1 ASP 19 C ASP 19 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc15 C O ASP 19 C ASP 19 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc16 C OD2 ASP 22 C ASP 22 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc17 C O GLY 23 C GLY 23 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc18 C N ASP 25 C ASP 25 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.318 ? metalc ? metalc19 C OD1 ASP 25 C ASP 25 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc20 C O ALA 27 C ALA 27 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? # _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 1KQM _atom_sites.fract_transf_matrix[1][1] 0.019085 _atom_sites.fract_transf_matrix[1][2] -0.000857 _atom_sites.fract_transf_matrix[1][3] -0.002453 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01707 _atom_sites.fract_transf_matrix[2][3] -0.002428 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006845 _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 D 4 MG A 1 903 903 MG MG . E 5 ANP A 1 999 999 ANP ANP . F 4 MG B 1 502 502 MG MG . G 6 CA C 1 501 501 CA CA . H 7 HOH A 1 1000 2 HOH HOH . H 7 HOH A 2 1001 3 HOH HOH . H 7 HOH A 3 1002 4 HOH HOH . H 7 HOH A 4 1003 6 HOH HOH . H 7 HOH A 5 1004 7 HOH HOH . I 7 HOH B 1 503 1 HOH HOH . J 7 HOH C 1 502 5 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 5 12.134 -8.235 27.985 1 36.38 ? PG ANP 999 A 1 HETATM 2 O O1G ANP . . . E 5 12.461 -6.907 27.329 1 17.4 ? O1G ANP 999 A 1 HETATM 3 O O2G ANP . . . E 5 10.852 -8.249 28.777 1 34.59 ? O2G ANP 999 A 1 HETATM 4 O O3G ANP . . . E 5 13.288 -8.765 28.812 1 18.98 ? O3G ANP 999 A 1 HETATM 5 P PB ANP . . . E 5 13.047 -10.373 26.028 1 17.67 ? PB ANP 999 A 1 HETATM 6 O O1B ANP . . . E 5 13.142 -10.194 24.597 1 9.05 ? O1B ANP 999 A 1 HETATM 7 O O2B ANP . . . E 5 14.391 -10.145 26.697 1 12.51 ? O2B ANP 999 A 1 HETATM 8 N N3B ANP . . . E 5 11.93 -9.331 26.698 1 16.27 ? N3B ANP 999 A 1 HETATM 9 P PA ANP . . . E 5 12.908 -12.904 27.536 1 17.25 ? PA ANP 999 A 1 HETATM 10 O O1A ANP . . . E 5 14.456 -12.781 27.767 1 20.15 ? O1A ANP 999 A 1 HETATM 11 O O2A ANP . . . E 5 12.085 -12.641 28.749 1 9.46 ? O2A ANP 999 A 1 HETATM 12 O O3A ANP . . . E 5 12.527 -11.87 26.36 1 22.44 ? O3A ANP 999 A 1 HETATM 13 O O5' ANP . . . E 5 12.598 -14.376 26.961 1 25.42 ? O5' ANP 999 A 1 HETATM 14 C C5' ANP . . . E 5 11.206 -14.749 26.795 1 17.65 ? C5' ANP 999 A 1 HETATM 15 C C4' ANP . . . E 5 11.013 -16.179 27.307 1 9.9 ? C4' ANP 999 A 1 HETATM 16 O O4' ANP . . . E 5 10.981 -17.039 26.157 1 23.21 ? O4' ANP 999 A 1 HETATM 17 C C3' ANP . . . E 5 12.244 -16.68 28.036 1 18.5 ? C3' ANP 999 A 1 HETATM 18 O O3' ANP . . . E 5 12.184 -16.292 29.404 1 20.2 ? O3' ANP 999 A 1 HETATM 19 C C2' ANP . . . E 5 12.079 -18.126 27.805 1 32.67 ? C2' ANP 999 A 1 HETATM 20 O O2' ANP . . . E 5 10.862 -18.53 28.479 1 38.82 ? O2' ANP 999 A 1 HETATM 21 C C1' ANP . . . E 5 11.782 -18.119 26.358 1 25.32 ? C1' ANP 999 A 1 HETATM 22 N N9 ANP . . . E 5 12.909 -18.151 25.45 1 26.13 ? N9 ANP 999 A 1 HETATM 23 C C8 ANP . . . E 5 13.448 -17.186 24.718 1 25.4 ? C8 ANP 999 A 1 HETATM 24 N N7 ANP . . . E 5 14.268 -17.641 23.779 1 23.16 ? N7 ANP 999 A 1 HETATM 25 C C5 ANP . . . E 5 14.317 -19.001 24.003 1 37.12 ? C5 ANP 999 A 1 HETATM 26 C C6 ANP . . . E 5 15.082 -20.059 23.393 1 23.53 ? C6 ANP 999 A 1 HETATM 27 N N6 ANP . . . E 5 15.949 -20.036 22.327 1 20.96 ? N6 ANP 999 A 1 HETATM 28 N N1 ANP . . . E 5 14.767 -21.253 23.927 1 30.6 ? N1 ANP 999 A 1 HETATM 29 C C2 ANP . . . E 5 13.906 -21.452 24.962 1 49.13 ? C2 ANP 999 A 1 HETATM 30 N N3 ANP . . . E 5 13.246 -20.501 25.557 1 27.2 ? N3 ANP 999 A 1 HETATM 31 C C4 ANP . . . E 5 13.5 -19.296 25.049 1 27.39 ? C4 ANP 999 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #