data_1K3A # _model_server_result.job_id 60cxp_t016cZsQdp1lJhxA _model_server_result.datetime_utc '2024-12-25 06:37:39' _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 1k3a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":300}' # _entry.id 1K3A # _exptl.entry_id 1K3A _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 90 _cell.angle_gamma 90 _cell.entry_id 1K3A _cell.length_a 80.624 _cell.length_b 111.018 _cell.length_c 93.297 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1K3A _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 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 _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 ILE 173 A ILE 1130 1_555 A N PTR 174 A PTR 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C PTR 174 A PTR 1131 1_555 A N GLU 175 A GLU 1132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 A C ASP 177 A ASP 1134 1_555 A N PTR 178 A PTR 1135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 A C PTR 178 A PTR 1135 1_555 A N PTR 179 A PTR 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C PTR 179 A PTR 1136 1_555 A N ARG 180 A ARG 1137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? # _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 1K3A _atom_sites.fract_transf_matrix[1][1] 0.012403 _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] 0.009008 _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] 0.010718 _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 1 300 300 ACP ACP . D 4 HOH A 1 1 1 HOH HOH . D 4 HOH A 2 2 2 HOH HOH . D 4 HOH A 3 3 3 HOH HOH . D 4 HOH A 4 4 4 HOH HOH . D 4 HOH A 5 5 5 HOH HOH . D 4 HOH A 6 6 6 HOH HOH . D 4 HOH A 7 7 7 HOH HOH . D 4 HOH A 8 8 8 HOH HOH . D 4 HOH A 9 9 9 HOH HOH . D 4 HOH A 10 10 10 HOH HOH . D 4 HOH A 11 11 11 HOH HOH . D 4 HOH A 12 12 12 HOH HOH . D 4 HOH A 13 13 13 HOH HOH . D 4 HOH A 14 14 14 HOH HOH . D 4 HOH A 15 15 15 HOH HOH . D 4 HOH A 16 16 16 HOH HOH . D 4 HOH A 17 17 17 HOH HOH . D 4 HOH A 18 18 18 HOH HOH . D 4 HOH A 19 19 19 HOH HOH . D 4 HOH A 20 20 20 HOH HOH . D 4 HOH A 21 21 21 HOH HOH . D 4 HOH A 22 22 22 HOH HOH . D 4 HOH A 23 23 23 HOH HOH . D 4 HOH A 24 24 24 HOH HOH . D 4 HOH A 25 25 25 HOH HOH . D 4 HOH A 26 26 26 HOH HOH . D 4 HOH A 27 28 28 HOH HOH . D 4 HOH A 28 29 29 HOH HOH . D 4 HOH A 29 30 30 HOH HOH . D 4 HOH A 30 31 31 HOH HOH . D 4 HOH A 31 32 32 HOH HOH . D 4 HOH A 32 33 33 HOH HOH . D 4 HOH A 33 34 34 HOH HOH . D 4 HOH A 34 35 35 HOH HOH . D 4 HOH A 35 36 36 HOH HOH . D 4 HOH A 36 37 37 HOH HOH . D 4 HOH A 37 38 38 HOH HOH . D 4 HOH A 38 39 39 HOH HOH . D 4 HOH A 39 40 40 HOH HOH . D 4 HOH A 40 41 41 HOH HOH . D 4 HOH A 41 43 43 HOH HOH . D 4 HOH A 42 44 44 HOH HOH . D 4 HOH A 43 45 45 HOH HOH . D 4 HOH A 44 47 47 HOH HOH . D 4 HOH A 45 48 48 HOH HOH . D 4 HOH A 46 49 49 HOH HOH . D 4 HOH A 47 50 50 HOH HOH . D 4 HOH A 48 52 52 HOH HOH . D 4 HOH A 49 53 53 HOH HOH . D 4 HOH A 50 54 54 HOH HOH . D 4 HOH A 51 55 55 HOH HOH . D 4 HOH A 52 56 56 HOH HOH . D 4 HOH A 53 57 57 HOH HOH . D 4 HOH A 54 58 58 HOH HOH . D 4 HOH A 55 59 59 HOH HOH . D 4 HOH A 56 60 60 HOH HOH . D 4 HOH A 57 61 61 HOH HOH . D 4 HOH A 58 62 62 HOH HOH . D 4 HOH A 59 63 63 HOH HOH . D 4 HOH A 60 64 64 HOH HOH . D 4 HOH A 61 65 65 HOH HOH . D 4 HOH A 62 66 66 HOH HOH . D 4 HOH A 63 67 67 HOH HOH . D 4 HOH A 64 69 69 HOH HOH . D 4 HOH A 65 70 70 HOH HOH . D 4 HOH A 66 71 71 HOH HOH . D 4 HOH A 67 72 72 HOH HOH . D 4 HOH A 68 73 73 HOH HOH . D 4 HOH A 69 74 74 HOH HOH . D 4 HOH A 70 75 75 HOH HOH . D 4 HOH A 71 76 76 HOH HOH . D 4 HOH A 72 77 77 HOH HOH . D 4 HOH A 73 78 78 HOH HOH . D 4 HOH A 74 79 79 HOH HOH . D 4 HOH A 75 80 80 HOH HOH . D 4 HOH A 76 81 81 HOH HOH . D 4 HOH A 77 82 82 HOH HOH . D 4 HOH A 78 83 83 HOH HOH . D 4 HOH A 79 84 84 HOH HOH . D 4 HOH A 80 85 85 HOH HOH . D 4 HOH A 81 86 86 HOH HOH . D 4 HOH A 82 87 87 HOH HOH . D 4 HOH A 83 88 88 HOH HOH . D 4 HOH A 84 89 89 HOH HOH . D 4 HOH A 85 90 90 HOH HOH . D 4 HOH A 86 91 91 HOH HOH . D 4 HOH A 87 92 92 HOH HOH . D 4 HOH A 88 93 93 HOH HOH . D 4 HOH A 89 94 94 HOH HOH . D 4 HOH A 90 95 95 HOH HOH . D 4 HOH A 91 97 97 HOH HOH . D 4 HOH A 92 98 98 HOH HOH . D 4 HOH A 93 100 100 HOH HOH . D 4 HOH A 94 101 101 HOH HOH . D 4 HOH A 95 102 102 HOH HOH . D 4 HOH A 96 103 103 HOH HOH . D 4 HOH A 97 104 104 HOH HOH . D 4 HOH A 98 105 105 HOH HOH . D 4 HOH A 99 106 106 HOH HOH . D 4 HOH A 100 107 107 HOH HOH . D 4 HOH A 101 108 108 HOH HOH . D 4 HOH A 102 109 109 HOH HOH . D 4 HOH A 103 110 110 HOH HOH . D 4 HOH A 104 111 111 HOH HOH . D 4 HOH A 105 112 112 HOH HOH . D 4 HOH A 106 113 113 HOH HOH . D 4 HOH A 107 114 114 HOH HOH . D 4 HOH A 108 116 116 HOH HOH . D 4 HOH A 109 117 117 HOH HOH . D 4 HOH A 110 118 118 HOH HOH . D 4 HOH A 111 119 119 HOH HOH . D 4 HOH A 112 121 121 HOH HOH . D 4 HOH A 113 122 122 HOH HOH . D 4 HOH A 114 123 123 HOH HOH . D 4 HOH A 115 124 124 HOH HOH . D 4 HOH A 116 126 126 HOH HOH . D 4 HOH A 117 127 127 HOH HOH . D 4 HOH A 118 128 128 HOH HOH . D 4 HOH A 119 129 129 HOH HOH . D 4 HOH A 120 130 130 HOH HOH . D 4 HOH A 121 131 131 HOH HOH . D 4 HOH A 122 132 132 HOH HOH . D 4 HOH A 123 133 133 HOH HOH . D 4 HOH A 124 134 134 HOH HOH . D 4 HOH A 125 135 135 HOH HOH . D 4 HOH A 126 136 136 HOH HOH . D 4 HOH A 127 137 137 HOH HOH . D 4 HOH A 128 138 138 HOH HOH . D 4 HOH A 129 139 139 HOH HOH . D 4 HOH A 130 140 140 HOH HOH . D 4 HOH A 131 141 141 HOH HOH . D 4 HOH A 132 142 142 HOH HOH . D 4 HOH A 133 143 143 HOH HOH . D 4 HOH A 134 144 144 HOH HOH . D 4 HOH A 135 145 145 HOH HOH . D 4 HOH A 136 146 146 HOH HOH . D 4 HOH A 137 147 147 HOH HOH . D 4 HOH A 138 148 148 HOH HOH . D 4 HOH A 139 149 149 HOH HOH . D 4 HOH A 140 150 150 HOH HOH . D 4 HOH A 141 151 151 HOH HOH . D 4 HOH A 142 152 152 HOH HOH . D 4 HOH A 143 153 153 HOH HOH . D 4 HOH A 144 154 154 HOH HOH . D 4 HOH A 145 155 155 HOH HOH . D 4 HOH A 146 156 156 HOH HOH . D 4 HOH A 147 157 157 HOH HOH . D 4 HOH A 148 158 158 HOH HOH . D 4 HOH A 149 159 159 HOH HOH . D 4 HOH A 150 160 160 HOH HOH . D 4 HOH A 151 164 164 HOH HOH . E 4 HOH B 1 27 27 HOH HOH . E 4 HOH B 2 42 42 HOH HOH . E 4 HOH B 3 51 51 HOH HOH . E 4 HOH B 4 96 96 HOH HOH . E 4 HOH B 5 99 99 HOH HOH . E 4 HOH B 6 115 115 HOH HOH . E 4 HOH B 7 125 125 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 28.187 20.375 47.993 1 90.63 ? PG ACP 300 A 1 HETATM 2 O O1G ACP . . . C 3 27.263 21.059 48.936 1 90.58 ? O1G ACP 300 A 1 HETATM 3 O O2G ACP . . . C 3 29.614 20.704 48.227 1 90.46 ? O2G ACP 300 A 1 HETATM 4 O O3G ACP . . . C 3 27.759 20.368 46.575 1 90.51 ? O3G ACP 300 A 1 HETATM 5 P PB ACP . . . C 3 28.989 17.539 47.592 1 88.83 ? PB ACP 300 A 1 HETATM 6 O O1B ACP . . . C 3 29.314 17.993 46.216 1 88.99 ? O1B ACP 300 A 1 HETATM 7 O O2B ACP . . . C 3 30.106 17.095 48.465 1 89.01 ? O2B ACP 300 A 1 HETATM 8 C C3B ACP . . . C 3 28.121 18.761 48.386 1 89.61 ? C3B ACP 300 A 1 HETATM 9 P PA ACP . . . C 3 26.836 16.029 48.383 1 84.52 ? PA ACP 300 A 1 HETATM 10 O O1A ACP . . . C 3 27.121 16.421 49.782 1 84.49 ? O1A ACP 300 A 1 HETATM 11 O O2A ACP . . . C 3 25.591 16.5 47.731 1 84.46 ? O2A ACP 300 A 1 HETATM 12 O O3A ACP . . . C 3 28.029 16.357 47.492 1 86.79 ? O3A ACP 300 A 1 HETATM 13 O O5' ACP . . . C 3 26.834 14.426 48.328 1 82.72 ? O5' ACP 300 A 1 HETATM 14 C C5' ACP . . . C 3 27.992 13.572 48.283 1 79.58 ? C5' ACP 300 A 1 HETATM 15 C C4' ACP . . . C 3 27.603 12.316 47.539 1 77.81 ? C4' ACP 300 A 1 HETATM 16 O O4' ACP . . . C 3 26.473 11.705 48.213 1 76.39 ? O4' ACP 300 A 1 HETATM 17 C C3' ACP . . . C 3 27.13 12.537 46.11 1 77.47 ? C3' ACP 300 A 1 HETATM 18 O O3' ACP . . . C 3 28.231 12.527 45.208 1 78.23 ? O3' ACP 300 A 1 HETATM 19 C C2' ACP . . . C 3 26.209 11.347 45.874 1 76.55 ? C2' ACP 300 A 1 HETATM 20 O O2' ACP . . . C 3 26.91 10.172 45.515 1 77.33 ? O2' ACP 300 A 1 HETATM 21 C C1' ACP . . . C 3 25.572 11.174 47.255 1 75.12 ? C1' ACP 300 A 1 HETATM 22 N N9 ACP . . . C 3 24.276 11.839 47.415 1 72.8 ? N9 ACP 300 A 1 HETATM 23 C C8 ACP . . . C 3 24.015 13.074 47.962 1 72.08 ? C8 ACP 300 A 1 HETATM 24 N N7 ACP . . . C 3 22.741 13.386 47.982 1 71.07 ? N7 ACP 300 A 1 HETATM 25 C C5 ACP . . . C 3 22.118 12.287 47.406 1 70.69 ? C5 ACP 300 A 1 HETATM 26 C C6 ACP . . . C 3 20.766 11.996 47.133 1 69.98 ? C6 ACP 300 A 1 HETATM 27 N N6 ACP . . . C 3 19.753 12.819 47.426 1 68.35 ? N6 ACP 300 A 1 HETATM 28 N N1 ACP . . . C 3 20.485 10.812 46.547 1 69.31 ? N1 ACP 300 A 1 HETATM 29 C C2 ACP . . . C 3 21.497 9.986 46.254 1 70.12 ? C2 ACP 300 A 1 HETATM 30 N N3 ACP . . . C 3 22.804 10.144 46.46 1 70.45 ? N3 ACP 300 A 1 HETATM 31 C C4 ACP . . . C 3 23.052 11.329 47.045 1 71.44 ? C4 ACP 300 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 555 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #