data_1KNY # _model_server_result.job_id EiwjCqYcKprOjA35qYV8JA _model_server_result.datetime_utc '2025-02-27 06:07:32' _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 1kny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":556}' # _entry.id 1KNY # _exptl.entry_id 1KNY _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 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL 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 1KNY _cell.length_a 57.3 _cell.length_b 102.2 _cell.length_c 108.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KNY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 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,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 # 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 G 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 OE2 GLU 52 A GLU 52 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 A OE1 GLU 52 A GLU 52 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc3 D O1G APC . A APC 556 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc4 D O2B APC . A APC 556 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc5 B OE1 GLU 52 B GLU 52 1_555 F MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.018 ? metalc ? metalc6 B OE2 GLU 52 B GLU 52 1_555 F MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc7 G O1G APC . B APC 557 1_555 F MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc8 G O2B APC . B APC 557 1_555 F MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 1KNY _atom_sites.fract_transf_matrix[1][1] 0.017452 _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] 0.009785 _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] 0.009191 _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 1 603 603 MG MG . D 3 APC A 1 556 556 APC APC . E 4 KAN A 1 558 558 KAN KAN . F 2 MG B 1 604 604 MG MG . G 3 APC B 1 557 557 APC APC . H 4 KAN B 1 559 559 KAN KAN . I 5 HOH A 1 604 1 HOH HOH . I 5 HOH A 2 605 2 HOH HOH . I 5 HOH A 3 606 3 HOH HOH . I 5 HOH A 4 607 4 HOH HOH . I 5 HOH A 5 608 5 HOH HOH . I 5 HOH A 6 609 6 HOH HOH . I 5 HOH A 7 610 7 HOH HOH . I 5 HOH A 8 611 12 HOH HOH . I 5 HOH A 9 612 14 HOH HOH . I 5 HOH A 10 613 15 HOH HOH . I 5 HOH A 11 614 16 HOH HOH . I 5 HOH A 12 615 17 HOH HOH . I 5 HOH A 13 616 18 HOH HOH . I 5 HOH A 14 617 19 HOH HOH . I 5 HOH A 15 618 20 HOH HOH . I 5 HOH A 16 619 21 HOH HOH . I 5 HOH A 17 620 22 HOH HOH . I 5 HOH A 18 621 23 HOH HOH . I 5 HOH A 19 622 24 HOH HOH . I 5 HOH A 20 623 25 HOH HOH . I 5 HOH A 21 624 34 HOH HOH . I 5 HOH A 22 625 35 HOH HOH . I 5 HOH A 23 626 36 HOH HOH . I 5 HOH A 24 627 37 HOH HOH . I 5 HOH A 25 628 38 HOH HOH . I 5 HOH A 26 629 39 HOH HOH . I 5 HOH A 27 630 40 HOH HOH . I 5 HOH A 28 631 42 HOH HOH . J 5 HOH B 1 605 8 HOH HOH . J 5 HOH B 2 606 9 HOH HOH . J 5 HOH B 3 607 10 HOH HOH . J 5 HOH B 4 608 11 HOH HOH . J 5 HOH B 5 609 13 HOH HOH . J 5 HOH B 6 610 26 HOH HOH . J 5 HOH B 7 611 27 HOH HOH . J 5 HOH B 8 612 28 HOH HOH . J 5 HOH B 9 613 29 HOH HOH . J 5 HOH B 10 614 30 HOH HOH . J 5 HOH B 11 615 31 HOH HOH . J 5 HOH B 12 616 32 HOH HOH . J 5 HOH B 13 617 33 HOH HOH . J 5 HOH B 14 618 41 HOH HOH . J 5 HOH B 15 619 43 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 APC . . . D 3 10.543 38.023 39.742 1 49.3 ? PG APC 556 A 1 HETATM 2 O O1G APC . . . D 3 10.229 39.084 40.763 1 53.82 ? O1G APC 556 A 1 HETATM 3 O O2G APC . . . D 3 9.417 37.039 39.648 1 31.41 ? O2G APC 556 A 1 HETATM 4 O O3G APC . . . D 3 11.892 37.257 40.146 1 35.49 ? O3G APC 556 A 1 HETATM 5 P PB APC . . . D 3 11.569 40.032 37.944 1 4.03 ? PB APC 556 A 1 HETATM 6 O O1B APC . . . D 3 11.941 39.987 36.484 1 51.91 ? O1B APC 556 A 1 HETATM 7 O O2B APC . . . D 3 10.782 41.253 38.244 1 38.32 ? O2B APC 556 A 1 HETATM 8 O O3B APC . . . D 3 10.73 38.722 38.325 1 23.15 ? O3B APC 556 A 1 HETATM 9 P PA APC . . . D 3 13.871 41.568 39.348 1 2.07 ? PA APC 556 A 1 HETATM 10 O O1A APC . . . D 3 14.082 41.66 40.823 1 37.11 ? O1A APC 556 A 1 HETATM 11 O O2A APC . . . D 3 15.213 41.603 38.679 1 58.56 ? O2A APC 556 A 1 HETATM 12 C C3A APC . . . D 3 13.066 40.018 38.942 1 56.33 ? C3A APC 556 A 1 HETATM 13 O O5' APC . . . D 3 12.991 42.806 38.865 1 52.26 ? O5' APC 556 A 1 HETATM 14 C C5' APC . . . D 3 13.739 43.852 38.236 1 32.17 ? C5' APC 556 A 1 HETATM 15 C C4' APC . . . D 3 13.065 44.307 36.964 1 22.78 ? C4' APC 556 A 1 HETATM 16 O O4' APC . . . D 3 13.595 45.629 36.656 1 31.66 ? O4' APC 556 A 1 HETATM 17 C C3' APC . . . D 3 13.332 43.43 35.741 1 100 ? C3' APC 556 A 1 HETATM 18 O O3' APC . . . D 3 12.225 42.541 35.469 1 36.7 ? O3' APC 556 A 1 HETATM 19 C C2' APC . . . D 3 13.641 44.454 34.636 1 81.75 ? C2' APC 556 A 1 HETATM 20 O O2' APC . . . D 3 12.491 44.714 33.819 1 56.09 ? O2' APC 556 A 1 HETATM 21 C C1' APC . . . D 3 14.029 45.731 35.351 1 89.64 ? C1' APC 556 A 1 HETATM 22 N N9 APC . . . D 3 15.462 46.069 35.404 1 15.89 ? N9 APC 556 A 1 HETATM 23 C C8 APC . . . D 3 16.005 47.33 35.306 1 100 ? C8 APC 556 A 1 HETATM 24 N N7 APC . . . D 3 17.307 47.372 35.513 1 58.89 ? N7 APC 556 A 1 HETATM 25 C C5 APC . . . D 3 17.642 46.063 35.907 1 76.93 ? C5 APC 556 A 1 HETATM 26 C C6 APC . . . D 3 18.892 45.484 36.269 1 25.1 ? C6 APC 556 A 1 HETATM 27 N N6 APC . . . D 3 19.961 46.062 36.388 1 100 ? N6 APC 556 A 1 HETATM 28 N N1 APC . . . D 3 18.777 44.15 36.331 1 100 ? N1 APC 556 A 1 HETATM 29 C C2 APC . . . D 3 17.646 43.402 36.197 1 100 ? C2 APC 556 A 1 HETATM 30 N N3 APC . . . D 3 16.505 43.905 35.937 1 7.34 ? N3 APC 556 A 1 HETATM 31 C C4 APC . . . D 3 16.55 45.234 35.727 1 100 ? C4 APC 556 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #