data_1KOF # _model_server_result.job_id VhU9CiVUZyH4_hqSUK867Q _model_server_result.datetime_utc '2025-08-04 10:36:08' _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 1kof # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1KOF # _exptl.entry_id 1KOF _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.76 _cell.angle_gamma 90 _cell.entry_id 1KOF _cell.length_a 42.74 _cell.length_b 88.41 _cell.length_c 51.48 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KOF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 OG SER 22 A SER 22 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc2 D O1B ACP . A ACP 500 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc3 D O2G ACP . A ACP 500 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc4 C MG MG . A MG 1001 1_555 G O HOH . A HOH 1023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc5 B OG SER 22 B SER 22 1_555 E MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc6 F O2G ACP . B ACP 501 1_555 E MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc7 F O1B ACP . B ACP 501 1_555 E MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? # _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 1KOF _atom_sites.fract_transf_matrix[1][1] 0.023397 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006603 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011311 _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] 0.020184 _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 1001 1 MG MG . D 3 ACP A 1 500 500 ACP ACP . E 2 MG B 1 1002 2 MG MG . F 3 ACP B 1 501 500 ACP ACP . G 4 HOH A 1 1002 3 HOH HOH . G 4 HOH A 2 1003 4 HOH HOH . G 4 HOH A 3 1004 5 HOH HOH . G 4 HOH A 4 1005 6 HOH HOH . G 4 HOH A 5 1006 10 HOH HOH . G 4 HOH A 6 1007 11 HOH HOH . G 4 HOH A 7 1008 14 HOH HOH . G 4 HOH A 8 1009 15 HOH HOH . G 4 HOH A 9 1010 17 HOH HOH . G 4 HOH A 10 1011 18 HOH HOH . G 4 HOH A 11 1012 22 HOH HOH . G 4 HOH A 12 1013 23 HOH HOH . G 4 HOH A 13 1014 24 HOH HOH . G 4 HOH A 14 1015 26 HOH HOH . G 4 HOH A 15 1016 28 HOH HOH . G 4 HOH A 16 1017 29 HOH HOH . G 4 HOH A 17 1018 32 HOH HOH . G 4 HOH A 18 1019 36 HOH HOH . G 4 HOH A 19 1020 37 HOH HOH . G 4 HOH A 20 1021 38 HOH HOH . G 4 HOH A 21 1022 40 HOH HOH . G 4 HOH A 22 1023 42 HOH HOH . G 4 HOH A 23 1024 43 HOH HOH . G 4 HOH A 24 1025 44 HOH HOH . G 4 HOH A 25 1026 45 HOH HOH . G 4 HOH A 26 1027 46 HOH HOH . G 4 HOH A 27 1028 48 HOH HOH . G 4 HOH A 28 1029 49 HOH HOH . G 4 HOH A 29 1030 52 HOH HOH . G 4 HOH A 30 1031 54 HOH HOH . G 4 HOH A 31 1032 57 HOH HOH . G 4 HOH A 32 1033 62 HOH HOH . G 4 HOH A 33 1034 65 HOH HOH . G 4 HOH A 34 1035 67 HOH HOH . H 4 HOH B 1 1003 7 HOH HOH . H 4 HOH B 2 1004 8 HOH HOH . H 4 HOH B 3 1005 9 HOH HOH . H 4 HOH B 4 1006 12 HOH HOH . H 4 HOH B 5 1007 13 HOH HOH . H 4 HOH B 6 1008 16 HOH HOH . H 4 HOH B 7 1009 19 HOH HOH . H 4 HOH B 8 1010 20 HOH HOH . H 4 HOH B 9 1011 21 HOH HOH . H 4 HOH B 10 1012 25 HOH HOH . H 4 HOH B 11 1013 27 HOH HOH . H 4 HOH B 12 1014 30 HOH HOH . H 4 HOH B 13 1015 31 HOH HOH . H 4 HOH B 14 1016 33 HOH HOH . H 4 HOH B 15 1017 34 HOH HOH . H 4 HOH B 16 1018 35 HOH HOH . H 4 HOH B 17 1019 39 HOH HOH . H 4 HOH B 18 1020 41 HOH HOH . H 4 HOH B 19 1021 47 HOH HOH . H 4 HOH B 20 1022 50 HOH HOH . H 4 HOH B 21 1023 51 HOH HOH . H 4 HOH B 22 1024 53 HOH HOH . H 4 HOH B 23 1025 55 HOH HOH . H 4 HOH B 24 1026 56 HOH HOH . H 4 HOH B 25 1027 58 HOH HOH . H 4 HOH B 26 1028 59 HOH HOH . H 4 HOH B 27 1029 60 HOH HOH . H 4 HOH B 28 1030 61 HOH HOH . H 4 HOH B 29 1031 63 HOH HOH . H 4 HOH B 30 1032 64 HOH HOH . H 4 HOH B 31 1033 66 HOH HOH . H 4 HOH B 32 1034 68 HOH HOH . H 4 HOH B 33 1035 69 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 . . . D 3 0.186 -14.617 16.708 1 58.8 ? PG ACP 500 A 1 HETATM 2 O O1G ACP . . . D 3 0.325 -14.404 18.202 1 59.13 ? O1G ACP 500 A 1 HETATM 3 O O2G ACP . . . D 3 0.743 -13.387 16.066 1 57.58 ? O2G ACP 500 A 1 HETATM 4 O O3G ACP . . . D 3 0.887 -15.809 16.169 1 51.68 ? O3G ACP 500 A 1 HETATM 5 P PB ACP . . . D 3 -2.572 -13.798 17.309 1 60.7 ? PB ACP 500 A 1 HETATM 6 O O1B ACP . . . D 3 -2.353 -12.306 17.176 1 58.15 ? O1B ACP 500 A 1 HETATM 7 O O2B ACP . . . D 3 -2.644 -14.103 18.799 1 55.54 ? O2B ACP 500 A 1 HETATM 8 C C3B ACP . . . D 3 -1.503 -14.764 16.343 1 57.34 ? C3B ACP 500 A 1 HETATM 9 P PA ACP . . . D 3 -4.529 -13.362 15.735 1 64.93 ? PA ACP 500 A 1 HETATM 10 O O1A ACP . . . D 3 -3.618 -12.819 14.663 1 65.78 ? O1A ACP 500 A 1 HETATM 11 O O2A ACP . . . D 3 -5.11 -12.209 16.492 1 63.07 ? O2A ACP 500 A 1 HETATM 12 O O3A ACP . . . D 3 -3.843 -14.239 16.713 1 62.26 ? O3A ACP 500 A 1 HETATM 13 O O5' ACP . . . D 3 -5.569 -14.263 15.125 1 66.59 ? O5' ACP 500 A 1 HETATM 14 C C5' ACP . . . D 3 -5.801 -15.589 15.619 1 68.84 ? C5' ACP 500 A 1 HETATM 15 C C4' ACP . . . D 3 -6.915 -16.25 14.799 1 68.03 ? C4' ACP 500 A 1 HETATM 16 O O4' ACP . . . D 3 -8.16 -16.075 15.419 1 66.41 ? O4' ACP 500 A 1 HETATM 17 C C3' ACP . . . D 3 -7.168 -15.474 13.518 1 67.83 ? C3' ACP 500 A 1 HETATM 18 O O3' ACP . . . D 3 -7.929 -16.306 12.659 1 69.2 ? O3' ACP 500 A 1 HETATM 19 C C2' ACP . . . D 3 -8.119 -14.392 13.906 1 64.1 ? C2' ACP 500 A 1 HETATM 20 O O2' ACP . . . D 3 -8.684 -14.028 12.674 1 65.49 ? O2' ACP 500 A 1 HETATM 21 C C1' ACP . . . D 3 -9.05 -15.171 14.782 1 62.84 ? C1' ACP 500 A 1 HETATM 22 N N9 ACP . . . D 3 -9.631 -14.58 16.005 1 62.67 ? N9 ACP 500 A 1 HETATM 23 C C8 ACP . . . D 3 -9.011 -13.898 16.985 1 60.53 ? C8 ACP 500 A 1 HETATM 24 N N7 ACP . . . D 3 -9.888 -13.567 17.971 1 60.46 ? N7 ACP 500 A 1 HETATM 25 C C5 ACP . . . D 3 -11.066 -14.1 17.651 1 59.96 ? C5 ACP 500 A 1 HETATM 26 C C6 ACP . . . D 3 -12.386 -14.162 18.249 1 59.18 ? C6 ACP 500 A 1 HETATM 27 N N6 ACP . . . D 3 -12.655 -13.557 19.464 1 61.07 ? N6 ACP 500 A 1 HETATM 28 N N1 ACP . . . D 3 -13.328 -14.82 17.595 1 61.7 ? N1 ACP 500 A 1 HETATM 29 C C2 ACP . . . D 3 -13.093 -15.417 16.422 1 61.7 ? C2 ACP 500 A 1 HETATM 30 N N3 ACP . . . D 3 -11.912 -15.375 15.793 1 59.81 ? N3 ACP 500 A 1 HETATM 31 C C4 ACP . . . D 3 -10.893 -14.771 16.364 1 60.83 ? C4 ACP 500 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #