data_1KF0 # _model_server_result.job_id WBuC-ZOJ_b8ASKKnElr74Q _model_server_result.datetime_utc '2024-11-06 05:34:17' _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 1kf0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":418}' # _entry.id 1KF0 # _exptl.entry_id 1KF0 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.9 _cell.angle_gamma 90 _cell.entry_id 1KF0 _cell.length_a 36.6 _cell.length_b 110.3 _cell.length_c 48 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KF0 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 4 _struct_asym.id D _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 metalc ? metalc1 A OD1 ASP 218 A ASP 218 1_555 B MG MG . A MG 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc2 D O2B ACP . A ACP 418 1_555 B MG MG . A MG 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? # _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 18 n n PG O2G ACP sing 19 n n PG O3G ACP sing 20 n n PG C3B ACP sing 21 n n O2G HOG2 ACP sing 22 n n O3G HOG3 ACP sing 23 n n PB O1B ACP doub 24 n n PB O2B ACP sing 25 n n PB C3B ACP sing 26 n n PB O3A ACP sing 27 n n O2B HOB2 ACP sing 28 n n C3B H3B1 ACP sing 29 n n C3B H3B2 ACP sing 30 n n PA O1A ACP doub 31 n n PA O2A ACP sing 32 n n PA O3A ACP sing 33 n n PA O5' ACP sing 34 n n O2A HOA2 ACP sing 35 n n O5' C5' ACP sing 36 n n C5' C4' ACP sing 37 n n C5' "H5'1" ACP sing 38 n n C5' "H5'2" ACP sing 39 n n C4' O4' ACP sing 40 n n C4' C3' ACP sing 41 n n C4' H4' ACP sing 42 n n O4' C1' ACP sing 43 n n C3' O3' ACP sing 44 n n C3' C2' ACP sing 45 n n C3' H3' ACP sing 46 n n O3' HO3' ACP sing 47 n n C2' O2' ACP sing 48 n n C2' C1' ACP sing 49 n n C2' H2' ACP sing 50 n n O2' HO2' ACP sing 51 n n C1' N9 ACP sing 52 n n C1' H1' ACP sing 53 n n N9 C8 ACP sing 54 n y N9 C4 ACP sing 55 n y C8 N7 ACP doub 56 n y C8 H8 ACP sing 57 n n N7 C5 ACP sing 58 n y C5 C6 ACP sing 59 n y C5 C4 ACP doub 60 n y C6 N6 ACP sing 61 n n C6 N1 ACP doub 62 n y N6 HN61 ACP sing 63 n n N6 HN62 ACP sing 64 n n N1 C2 ACP sing 65 n y C2 N3 ACP doub 66 n y C2 H2 ACP sing 67 n n N3 C4 ACP sing 68 n y # _atom_sites.entry_id 1KF0 _atom_sites.fract_transf_matrix[1][1] 0.027322 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001863 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009066 _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] 0.020882 _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 B 2 MG A 1 518 518 MG MG . C 3 3PG A 1 417 417 3PG MP3 . D 4 ACP A 1 418 418 ACP ACP . E 5 HOH A 1 419 419 HOH HOH . E 5 HOH A 2 420 420 HOH HOH . E 5 HOH A 3 421 421 HOH HOH . E 5 HOH A 4 422 422 HOH HOH . E 5 HOH A 5 423 423 HOH HOH . E 5 HOH A 6 424 424 HOH HOH . E 5 HOH A 7 425 425 HOH HOH . E 5 HOH A 8 426 426 HOH HOH . E 5 HOH A 9 427 427 HOH HOH . E 5 HOH A 10 428 428 HOH HOH . E 5 HOH A 11 429 429 HOH HOH . E 5 HOH A 12 430 430 HOH HOH . E 5 HOH A 13 431 431 HOH HOH . E 5 HOH A 14 432 432 HOH HOH . E 5 HOH A 15 433 433 HOH HOH . E 5 HOH A 16 435 435 HOH HOH . E 5 HOH A 17 436 436 HOH HOH . E 5 HOH A 18 438 438 HOH HOH . E 5 HOH A 19 439 439 HOH HOH . E 5 HOH A 20 440 440 HOH HOH . E 5 HOH A 21 441 441 HOH HOH . E 5 HOH A 22 442 442 HOH HOH . E 5 HOH A 23 443 443 HOH HOH . E 5 HOH A 24 444 444 HOH HOH . E 5 HOH A 25 445 445 HOH HOH . E 5 HOH A 26 446 446 HOH HOH . E 5 HOH A 27 447 447 HOH HOH . E 5 HOH A 28 448 448 HOH HOH . E 5 HOH A 29 449 449 HOH HOH . E 5 HOH A 30 450 450 HOH HOH . E 5 HOH A 31 451 451 HOH HOH . E 5 HOH A 32 452 452 HOH HOH . E 5 HOH A 33 453 453 HOH HOH . E 5 HOH A 34 454 454 HOH HOH . E 5 HOH A 35 455 455 HOH HOH . E 5 HOH A 36 456 456 HOH HOH . E 5 HOH A 37 457 457 HOH HOH . E 5 HOH A 38 458 458 HOH HOH . E 5 HOH A 39 459 459 HOH HOH . E 5 HOH A 40 460 460 HOH HOH . E 5 HOH A 41 461 461 HOH HOH . E 5 HOH A 42 462 462 HOH HOH . E 5 HOH A 43 463 463 HOH HOH . E 5 HOH A 44 464 464 HOH HOH . E 5 HOH A 45 465 465 HOH HOH . E 5 HOH A 46 466 466 HOH HOH . E 5 HOH A 47 467 467 HOH HOH . E 5 HOH A 48 468 468 HOH HOH . E 5 HOH A 49 469 469 HOH HOH . E 5 HOH A 50 470 470 HOH HOH . E 5 HOH A 51 471 471 HOH HOH . E 5 HOH A 52 472 472 HOH HOH . E 5 HOH A 53 473 473 HOH HOH . E 5 HOH A 54 474 474 HOH HOH . E 5 HOH A 55 475 475 HOH HOH . E 5 HOH A 56 476 476 HOH HOH . E 5 HOH A 57 477 477 HOH HOH . E 5 HOH A 58 478 478 HOH HOH . E 5 HOH A 59 480 480 HOH HOH . E 5 HOH A 60 481 481 HOH HOH . E 5 HOH A 61 482 482 HOH HOH . E 5 HOH A 62 483 483 HOH HOH . E 5 HOH A 63 484 484 HOH HOH . E 5 HOH A 64 485 485 HOH HOH . E 5 HOH A 65 486 486 HOH HOH . E 5 HOH A 66 487 487 HOH HOH . E 5 HOH A 67 488 488 HOH HOH . E 5 HOH A 68 489 489 HOH HOH . E 5 HOH A 69 490 490 HOH HOH . E 5 HOH A 70 491 491 HOH HOH . E 5 HOH A 71 493 493 HOH HOH . E 5 HOH A 72 494 494 HOH HOH . E 5 HOH A 73 495 495 HOH HOH . E 5 HOH A 74 496 496 HOH HOH . E 5 HOH A 75 500 500 HOH HOH . E 5 HOH A 76 501 501 HOH HOH . E 5 HOH A 77 502 502 HOH HOH . E 5 HOH A 78 503 503 HOH HOH . E 5 HOH A 79 504 504 HOH HOH . E 5 HOH A 80 505 505 HOH HOH . E 5 HOH A 81 506 506 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 4 9.565 -0.721 24.499 1 63.13 ? PG ACP 418 A 1 HETATM 2 O O1G ACP . . . D 4 9.558 -1.943 25.331 1 63.13 ? O1G ACP 418 A 1 HETATM 3 O O2G ACP . . . D 4 8.219 -0.153 24.276 1 63.13 ? O2G ACP 418 A 1 HETATM 4 O O3G ACP . . . D 4 10.568 0.277 24.922 1 63.13 ? O3G ACP 418 A 1 HETATM 5 P PB ACP . . . D 4 9.739 -0.194 21.412 1 63.13 ? PB ACP 418 A 1 HETATM 6 O O1B ACP . . . D 4 8.658 -0.862 20.62 1 63.13 ? O1B ACP 418 A 1 HETATM 7 O O2B ACP . . . D 4 11.043 0.163 20.753 1 63.13 ? O2B ACP 418 A 1 HETATM 8 C C3B ACP . . . D 4 10.132 -1.288 22.841 1 63.13 ? C3B ACP 418 A 1 HETATM 9 P PA ACP . . . D 4 9.459 2.669 21.95 1 63.13 ? PA ACP 418 A 1 HETATM 10 O O1A ACP . . . D 4 10.704 2.902 22.689 1 63.13 ? O1A ACP 418 A 1 HETATM 11 O O2A ACP . . . D 4 9.313 3.158 20.572 1 63.13 ? O2A ACP 418 A 1 HETATM 12 O O3A ACP . . . D 4 9.131 1.116 21.979 1 63.13 ? O3A ACP 418 A 1 HETATM 13 O O5' ACP . . . D 4 8.272 3.209 22.806 1 31.06 ? O5' ACP 418 A 1 HETATM 14 C C5' ACP . . . D 4 6.895 3.142 22.385 1 31.06 ? C5' ACP 418 A 1 HETATM 15 C C4' ACP . . . D 4 6.038 2.865 23.582 1 31.06 ? C4' ACP 418 A 1 HETATM 16 O O4' ACP . . . D 4 6.196 3.995 24.46 1 31.06 ? O4' ACP 418 A 1 HETATM 17 C C3' ACP . . . D 4 4.559 2.768 23.298 1 31.06 ? C3' ACP 418 A 1 HETATM 18 O O3' ACP . . . D 4 4.112 1.418 23.526 1 31.06 ? O3' ACP 418 A 1 HETATM 19 C C2' ACP . . . D 4 3.921 3.781 24.232 1 31.06 ? C2' ACP 418 A 1 HETATM 20 O O2' ACP . . . D 4 2.82 3.269 24.972 1 31.06 ? O2' ACP 418 A 1 HETATM 21 C C1' ACP . . . D 4 5.027 4.122 25.254 1 31.06 ? C1' ACP 418 A 1 HETATM 22 N N9 ACP . . . D 4 4.96 5.518 25.78 1 18.43 ? N9 ACP 418 A 1 HETATM 23 C C8 ACP . . . D 4 4.844 6.706 25.093 1 18.43 ? C8 ACP 418 A 1 HETATM 24 N N7 ACP . . . D 4 4.811 7.771 25.834 1 18.43 ? N7 ACP 418 A 1 HETATM 25 C C5 ACP . . . D 4 4.912 7.254 27.112 1 18.43 ? C5 ACP 418 A 1 HETATM 26 C C6 ACP . . . D 4 4.937 7.866 28.401 1 18.43 ? C6 ACP 418 A 1 HETATM 27 N N6 ACP . . . D 4 4.853 9.181 28.534 1 18.43 ? N6 ACP 418 A 1 HETATM 28 N N1 ACP . . . D 4 5.048 7.074 29.501 1 18.43 ? N1 ACP 418 A 1 HETATM 29 C C2 ACP . . . D 4 5.132 5.746 29.351 1 18.43 ? C2 ACP 418 A 1 HETATM 30 N N3 ACP . . . D 4 5.12 5.043 28.2 1 18.43 ? N3 ACP 418 A 1 HETATM 31 C C4 ACP . . . D 4 5.006 5.88 27.098 1 18.43 ? C4 ACP 418 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 46 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #