data_5EG3 # _model_server_result.job_id SsAKuQzXGffQ1hNAGIuNkg _model_server_result.datetime_utc '2024-10-20 19:49:27' _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 5eg3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":801}' # _entry.id 5EG3 # _exptl.entry_id 5EG3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _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 100.11 _cell.angle_gamma 90 _cell.entry_id 5EG3 _cell.length_a 79.609 _cell.length_b 53.231 _cell.length_c 127.66 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EG3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 3 _struct_asym.id C _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 GLU 324 A GLU 768 1_555 A N PTR 325 A PTR 769 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C PTR 325 A PTR 769 1_555 A N LEU 326 A LEU 770 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? metalc ? metalc1 A O ARG 186 A ARG 630 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? metalc ? metalc2 A OD1 ASN 187 A ASN 631 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc3 A OD1 ASN 187 A ASN 631 1_555 E MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc4 A OD2 ASP 200 A ASP 644 1_555 E MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc5 C O1A ACP . A ACP 801 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc6 C O1B ACP . A ACP 801 1_555 E MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc7 C O1A ACP . A ACP 801 1_555 E MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? # _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 5EG3 _atom_sites.fract_transf_matrix[1][1] 0.012561 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00224 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018786 _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] 0.007957 _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 3 ACP A 1 801 301 ACP ACP . D 4 MG A 1 802 1 MG MG . E 4 MG A 1 803 2 MG MG . F 5 HOH A 1 901 2 HOH HOH . F 5 HOH A 2 902 36 HOH HOH . F 5 HOH A 3 903 1 HOH HOH . F 5 HOH A 4 904 28 HOH HOH . F 5 HOH A 5 905 3 HOH HOH . F 5 HOH A 6 906 25 HOH HOH . F 5 HOH A 7 907 20 HOH HOH . F 5 HOH A 8 908 6 HOH HOH . F 5 HOH A 9 909 21 HOH HOH . F 5 HOH A 10 910 50 HOH HOH . F 5 HOH A 11 911 5 HOH HOH . F 5 HOH A 12 912 33 HOH HOH . F 5 HOH A 13 913 17 HOH HOH . F 5 HOH A 14 914 34 HOH HOH . F 5 HOH A 15 915 15 HOH HOH . F 5 HOH A 16 916 16 HOH HOH . F 5 HOH A 17 917 19 HOH HOH . F 5 HOH A 18 918 12 HOH HOH . F 5 HOH A 19 919 13 HOH HOH . F 5 HOH A 20 920 10 HOH HOH . F 5 HOH A 21 921 22 HOH HOH . F 5 HOH A 22 922 8 HOH HOH . F 5 HOH A 23 923 42 HOH HOH . F 5 HOH A 24 924 11 HOH HOH . F 5 HOH A 25 925 29 HOH HOH . F 5 HOH A 26 926 9 HOH HOH . F 5 HOH A 27 927 32 HOH HOH . F 5 HOH A 28 928 7 HOH HOH . F 5 HOH A 29 929 27 HOH HOH . F 5 HOH A 30 930 24 HOH HOH . F 5 HOH A 31 931 30 HOH HOH . F 5 HOH A 32 932 4 HOH HOH . F 5 HOH A 33 933 49 HOH HOH . F 5 HOH A 34 934 35 HOH HOH . F 5 HOH A 35 935 23 HOH HOH . F 5 HOH A 36 936 14 HOH HOH . F 5 HOH A 37 937 44 HOH HOH . F 5 HOH A 38 938 31 HOH HOH . F 5 HOH A 39 939 26 HOH HOH . G 5 HOH B 1 801 47 HOH HOH . G 5 HOH B 2 802 53 HOH HOH . G 5 HOH B 3 803 45 HOH HOH . G 5 HOH B 4 804 39 HOH HOH . G 5 HOH B 5 805 54 HOH HOH . G 5 HOH B 6 806 37 HOH HOH . G 5 HOH B 7 807 51 HOH HOH . G 5 HOH B 8 808 43 HOH HOH . G 5 HOH B 9 809 18 HOH HOH . G 5 HOH B 10 810 41 HOH HOH . G 5 HOH B 11 811 55 HOH HOH . G 5 HOH B 12 812 46 HOH HOH . G 5 HOH B 13 813 38 HOH HOH . G 5 HOH B 14 814 48 HOH HOH . G 5 HOH B 15 815 40 HOH HOH . G 5 HOH B 16 816 52 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 . . . C 3 20.197 -7.74 42.993 1 74.33 ? PG ACP 801 A 1 HETATM 2 O O1G ACP . . . C 3 21.11 -7.915 41.727 1 65.5 ? O1G ACP 801 A 1 HETATM 3 O O2G ACP . . . C 3 20.762 -8.616 44.155 1 56.49 ? O2G ACP 801 A 1 HETATM 4 O O3G ACP . . . C 3 20.219 -6.312 43.429 1 74.33 ? O3G ACP 801 A 1 HETATM 5 P PB ACP . . . C 3 17.975 -6.745 41.424 1 50.45 ? PB ACP 801 A 1 HETATM 6 O O1B ACP . . . C 3 18.815 -6.72 40.111 1 21.76 ? O1B ACP 801 A 1 HETATM 7 O O2B ACP . . . C 3 16.565 -7.084 41.091 1 51.06 ? O2B ACP 801 A 1 HETATM 8 C C3B ACP . . . C 3 18.457 -8.15 42.562 1 23.59 ? C3B ACP 801 A 1 HETATM 9 P PA ACP . . . C 3 17.836 -3.905 40.887 1 25.32 ? PA ACP 801 A 1 HETATM 10 O O1A ACP . . . C 3 18.752 -3.907 39.672 1 23.75 ? O1A ACP 801 A 1 HETATM 11 O O2A ACP . . . C 3 18.029 -2.601 41.63 1 24.17 ? O2A ACP 801 A 1 HETATM 12 O O3A ACP . . . C 3 18.141 -5.209 41.87 1 25.01 ? O3A ACP 801 A 1 HETATM 13 O O5' ACP . . . C 3 16.36 -3.859 40.308 1 30.32 ? O5' ACP 801 A 1 HETATM 14 C C5' ACP . . . C 3 16.303 -3.181 39.081 1 30.06 ? C5' ACP 801 A 1 HETATM 15 C C4' ACP . . . C 3 15.016 -3.226 38.359 1 29.3 ? C4' ACP 801 A 1 HETATM 16 O O4' ACP . . . C 3 13.851 -2.833 39.192 1 30.27 ? O4' ACP 801 A 1 HETATM 17 C C3' ACP . . . C 3 15.171 -2.244 37.312 1 28.05 ? C3' ACP 801 A 1 HETATM 18 O O3' ACP . . . C 3 15.407 -2.944 36.102 1 29.09 ? O3' ACP 801 A 1 HETATM 19 C C2' ACP . . . C 3 13.977 -1.48 37.269 1 28.65 ? C2' ACP 801 A 1 HETATM 20 O O2' ACP . . . C 3 13.115 -2.079 36.287 1 29.02 ? O2' ACP 801 A 1 HETATM 21 C C1' ACP . . . C 3 13.414 -1.528 38.622 1 29.18 ? C1' ACP 801 A 1 HETATM 22 N N9 ACP . . . C 3 13.884 -0.45 39.415 1 27.9 ? N9 ACP 801 A 1 HETATM 23 C C8 ACP . . . C 3 14.867 -0.466 40.341 1 27.99 ? C8 ACP 801 A 1 HETATM 24 N N7 ACP . . . C 3 15.032 0.757 40.857 1 27.73 ? N7 ACP 801 A 1 HETATM 25 C C5 ACP . . . C 3 14.169 1.61 40.302 1 26.78 ? C5 ACP 801 A 1 HETATM 26 C C6 ACP . . . C 3 13.884 2.987 40.435 1 27.75 ? C6 ACP 801 A 1 HETATM 27 N N6 ACP . . . C 3 14.606 3.844 41.357 1 27.75 ? N6 ACP 801 A 1 HETATM 28 N N1 ACP . . . C 3 12.924 3.54 39.693 1 27.79 ? N1 ACP 801 A 1 HETATM 29 C C2 ACP . . . C 3 12.219 2.817 38.805 1 25.63 ? C2 ACP 801 A 1 HETATM 30 N N3 ACP . . . C 3 12.459 1.491 38.643 1 25.51 ? N3 ACP 801 A 1 HETATM 31 C C4 ACP . . . C 3 13.416 0.858 39.367 1 25.4 ? C4 ACP 801 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #