data_5KSD # _model_server_result.job_id '_MF342H3GksqPnExIYaNRA' _model_server_result.datetime_utc '2024-10-28 02:28:39' _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 5ksd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":904}' # _entry.id 5KSD # _exptl.entry_id 5KSD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC 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 5KSD _cell.length_a 85.29 _cell.length_b 144.42 _cell.length_c 312.11 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G 1 1 B,H,I,J,K,L 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 K 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 metalc ? metalc1 A OD1 ASP 361 A ASP 372 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc2 A OD2 ASP 361 A ASP 372 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc3 A OD2 ASP 577 A ASP 588 1_555 C MG MG . A MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc4 A O LEU 585 A LEU 596 1_555 E K K . A K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.139 ? metalc ? metalc5 A O LYS 586 A LYS 597 1_555 E K K . A K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc6 A O ALA 588 A ALA 599 1_555 E K K . A K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc7 A OD1 ASP 606 A ASP 617 1_555 E K K . A K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc8 A OD2 ASP 606 A ASP 617 1_555 E K K . A K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc9 C MG MG . A MG 901 1_555 F O1B ACP . A ACP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc10 C MG MG . A MG 901 1_555 F O1G ACP . A ACP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc11 B OD2 ASP 577 B ASP 588 1_555 H MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc12 B O LEU 585 B LEU 596 1_555 J K K . B K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.152 ? metalc ? metalc13 B O LYS 586 B LYS 597 1_555 J K K . B K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc14 B O ALA 588 B ALA 599 1_555 J K K . B K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc15 B OD1 ASP 606 B ASP 617 1_555 J K K . B K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc16 B OD2 ASP 606 B ASP 617 1_555 J K K . B K 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc17 H MG MG . B MG 901 1_555 K O2G ACP . B ACP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc18 H MG MG . B MG 901 1_555 K O2B ACP . B ACP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc19 I MG MG . B MG 902 1_555 K O2A ACP . B ACP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? # _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 5KSD _atom_sites.fract_transf_matrix[1][1] 0.011725 _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] 0.006924 _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] 0.003204 _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 MG A 1 901 1002 MG MG . D 2 MG A 1 902 1003 MG MG . E 3 K A 1 903 1005 K K . F 4 ACP A 1 904 1001 ACP ACP . G 5 LMT A 1 905 1007 LMT LMT . H 2 MG B 1 901 1002 MG MG . I 2 MG B 1 902 1003 MG MG . J 3 K B 1 903 1005 K K . K 4 ACP B 1 904 1004 ACP ACP . L 5 LMT B 1 905 1007 LMT LMT . # 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 . . . K 4 18.989 -29.567 56.853 1 156.77 ? PG ACP 904 B 1 HETATM 2 O O1G ACP . . . K 4 20.198 -29.196 56 1 158.85 ? O1G ACP 904 B 1 HETATM 3 O O2G ACP . . . K 4 19.429 -30.356 58.094 1 193.45 ? O2G ACP 904 B 1 HETATM 4 O O3G ACP . . . K 4 18.273 -28.314 57.263 1 97.76 ? O3G ACP 904 B 1 HETATM 5 P PB ACP . . . K 4 18.633 -32.282 55.63 1 125.08 ? PB ACP 904 B 1 HETATM 6 O O1B ACP . . . K 4 20.049 -32.127 55.209 1 74.84 ? O1B ACP 904 B 1 HETATM 7 O O2B ACP . . . K 4 18.548 -33.061 56.906 1 140.55 ? O2B ACP 904 B 1 HETATM 8 C C3B ACP . . . K 4 17.856 -30.616 55.863 1 94.96 ? C3B ACP 904 B 1 HETATM 9 P PA ACP . . . K 4 17.653 -34.69 54.297 1 145.01 ? PA ACP 904 B 1 HETATM 10 O O1A ACP . . . K 4 18.896 -35.337 54.778 1 145.41 ? O1A ACP 904 B 1 HETATM 11 O O2A ACP . . . K 4 16.495 -35.17 55.076 1 161.72 ? O2A ACP 904 B 1 HETATM 12 O O3A ACP . . . K 4 17.768 -33.066 54.448 1 114.63 ? O3A ACP 904 B 1 HETATM 13 O O5' ACP . . . K 4 17.404 -35.029 52.679 1 149.34 ? O5' ACP 904 B 1 HETATM 14 C C5' ACP . . . K 4 18.461 -34.795 51.765 1 160.22 ? C5' ACP 904 B 1 HETATM 15 C C4' ACP . . . K 4 17.926 -34.968 50.324 1 134.67 ? C4' ACP 904 B 1 HETATM 16 O O4' ACP . . . K 4 17.008 -35.884 50.284 1 121.05 ? O4' ACP 904 B 1 HETATM 17 C C3' ACP . . . K 4 17.261 -33.629 49.88 1 112.24 ? C3' ACP 904 B 1 HETATM 18 O O3' ACP . . . K 4 17.556 -33.346 48.582 1 112.56 ? O3' ACP 904 B 1 HETATM 19 C C2' ACP . . . K 4 15.777 -33.891 50.021 1 107.44 ? C2' ACP 904 B 1 HETATM 20 O O2' ACP . . . K 4 15 -33.102 48.988 1 118.12 ? O2' ACP 904 B 1 HETATM 21 C C1' ACP . . . K 4 15.641 -35.182 49.8 1 119.67 ? C1' ACP 904 B 1 HETATM 22 N N9 ACP . . . K 4 14.523 -35.703 50.569 1 130.68 ? N9 ACP 904 B 1 HETATM 23 C C8 ACP . . . K 4 14.192 -35.379 51.839 1 153.83 ? C8 ACP 904 B 1 HETATM 24 N N7 ACP . . . K 4 13.091 -36.079 52.184 1 150.08 ? N7 ACP 904 B 1 HETATM 25 C C5 ACP . . . K 4 12.742 -36.833 51.136 1 132.53 ? C5 ACP 904 B 1 HETATM 26 C C6 ACP . . . K 4 11.709 -37.727 50.945 1 143.37 ? C6 ACP 904 B 1 HETATM 27 N N6 ACP . . . K 4 10.554 -38.241 51.789 1 158.84 ? N6 ACP 904 B 1 HETATM 28 N N1 ACP . . . K 4 11.583 -38.362 49.777 1 138.21 ? N1 ACP 904 B 1 HETATM 29 C C2 ACP . . . K 4 12.474 -38.131 48.769 1 138.65 ? C2 ACP 904 B 1 HETATM 30 N N3 ACP . . . K 4 13.501 -37.243 48.959 1 131.29 ? N3 ACP 904 B 1 HETATM 31 C C4 ACP . . . K 4 13.63 -36.599 50.132 1 128.18 ? C4 ACP 904 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #