data_5KPT # _model_server_result.job_id IcvyIMPN0dZeoJU5nw6Xwg _model_server_result.datetime_utc '2024-10-11 13:26:10' _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 5kpt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5KPT # _exptl.entry_id 5KPT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 120 _cell.entry_id 5KPT _cell.length_a 97.463 _cell.length_b 97.463 _cell.length_c 68.161 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KPT _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -45.440667 # _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 metalc ? metalc1 B MG MG . A MG 401 1_555 C O3G ANP . A ANP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc2 B MG MG . A MG 401 1_555 C O2B ANP . A ANP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc3 B MG MG . A MG 401 1_555 E O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc4 B MG MG . A MG 401 1_555 E O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc5 B MG MG . A MG 401 1_555 E O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc6 B MG MG . A MG 401 1_555 E O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 5KPT _atom_sites.fract_transf_matrix[1][1] 0.01026 _atom_sites.fract_transf_matrix[1][2] 0.005924 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011848 _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] 0.014671 _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 1 401 1 MG MG . C 3 ANP A 1 402 501 ANP ANP . D 4 EDO A 1 403 1 EDO EDO . E 5 HOH A 1 501 28 HOH HOH . E 5 HOH A 2 502 2 HOH HOH . E 5 HOH A 3 503 72 HOH HOH . E 5 HOH A 4 504 1 HOH HOH . E 5 HOH A 5 505 10 HOH HOH . E 5 HOH A 6 506 22 HOH HOH . E 5 HOH A 7 507 3 HOH HOH . E 5 HOH A 8 508 53 HOH HOH . E 5 HOH A 9 509 33 HOH HOH . E 5 HOH A 10 510 56 HOH HOH . E 5 HOH A 11 511 5 HOH HOH . E 5 HOH A 12 512 71 HOH HOH . E 5 HOH A 13 513 12 HOH HOH . E 5 HOH A 14 514 25 HOH HOH . E 5 HOH A 15 515 98 HOH HOH . E 5 HOH A 16 516 48 HOH HOH . E 5 HOH A 17 517 26 HOH HOH . E 5 HOH A 18 518 51 HOH HOH . E 5 HOH A 19 519 17 HOH HOH . E 5 HOH A 20 520 34 HOH HOH . E 5 HOH A 21 521 44 HOH HOH . E 5 HOH A 22 522 81 HOH HOH . E 5 HOH A 23 523 52 HOH HOH . E 5 HOH A 24 524 88 HOH HOH . E 5 HOH A 25 525 4 HOH HOH . E 5 HOH A 26 526 20 HOH HOH . E 5 HOH A 27 527 31 HOH HOH . E 5 HOH A 28 528 11 HOH HOH . E 5 HOH A 29 529 42 HOH HOH . E 5 HOH A 30 530 35 HOH HOH . E 5 HOH A 31 531 47 HOH HOH . E 5 HOH A 32 532 55 HOH HOH . E 5 HOH A 33 533 54 HOH HOH . E 5 HOH A 34 534 50 HOH HOH . E 5 HOH A 35 535 21 HOH HOH . E 5 HOH A 36 536 63 HOH HOH . E 5 HOH A 37 537 68 HOH HOH . E 5 HOH A 38 538 36 HOH HOH . E 5 HOH A 39 539 49 HOH HOH . E 5 HOH A 40 540 95 HOH HOH . E 5 HOH A 41 541 45 HOH HOH . E 5 HOH A 42 542 30 HOH HOH . E 5 HOH A 43 543 86 HOH HOH . E 5 HOH A 44 544 57 HOH HOH . E 5 HOH A 45 545 69 HOH HOH . E 5 HOH A 46 546 19 HOH HOH . E 5 HOH A 47 547 85 HOH HOH . E 5 HOH A 48 548 43 HOH HOH . E 5 HOH A 49 549 84 HOH HOH . E 5 HOH A 50 550 87 HOH HOH . E 5 HOH A 51 551 32 HOH HOH . E 5 HOH A 52 552 9 HOH HOH . E 5 HOH A 53 553 15 HOH HOH . E 5 HOH A 54 554 82 HOH HOH . E 5 HOH A 55 555 96 HOH HOH . E 5 HOH A 56 556 83 HOH HOH . E 5 HOH A 57 557 80 HOH HOH . E 5 HOH A 58 558 89 HOH HOH . E 5 HOH A 59 559 77 HOH HOH . E 5 HOH A 60 560 79 HOH HOH . E 5 HOH A 61 561 65 HOH HOH . E 5 HOH A 62 562 97 HOH HOH . E 5 HOH A 63 563 14 HOH HOH . E 5 HOH A 64 564 92 HOH HOH . E 5 HOH A 65 565 8 HOH HOH . E 5 HOH A 66 566 13 HOH HOH . E 5 HOH A 67 567 99 HOH HOH . E 5 HOH A 68 568 93 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 ANP . . . C 3 -26.532 17.452 -13.278 1 24.84 ? PG ANP 402 A 1 HETATM 2 O O1G ANP . . . C 3 -25.862 17.996 -14.513 1 31.18 ? O1G ANP 402 A 1 HETATM 3 O O2G ANP . . . C 3 -27.693 16.499 -13.707 1 24.21 ? O2G ANP 402 A 1 HETATM 4 O O3G ANP . . . C 3 -27.174 18.638 -12.489 1 33.26 ? O3G ANP 402 A 1 HETATM 5 P PB ANP . . . C 3 -25.281 16.506 -10.79 1 21.95 ? PB ANP 402 A 1 HETATM 6 O O1B ANP . . . C 3 -25.141 15.024 -10.417 1 22.54 ? O1B ANP 402 A 1 HETATM 7 O O2B ANP . . . C 3 -26.493 17.191 -10.102 1 33.51 ? O2B ANP 402 A 1 HETATM 8 N N3B ANP . . . C 3 -25.368 16.597 -12.456 1 30.61 ? N3B ANP 402 A 1 HETATM 9 P PA ANP . . . C 3 -23.444 17.68 -9.008 1 27.56 ? PA ANP 402 A 1 HETATM 10 O O1A ANP . . . C 3 -23.933 19.126 -8.741 1 30.07 ? O1A ANP 402 A 1 HETATM 11 O O2A ANP . . . C 3 -23.914 16.723 -7.857 1 22.97 ? O2A ANP 402 A 1 HETATM 12 O O3A ANP . . . C 3 -23.951 17.207 -10.403 1 28.26 ? O3A ANP 402 A 1 HETATM 13 O O5' ANP . . . C 3 -21.886 17.653 -9.126 1 29.82 ? O5' ANP 402 A 1 HETATM 14 C C5' ANP . . . C 3 -21.25 16.601 -9.788 1 22.07 ? C5' ANP 402 A 1 HETATM 15 C C4' ANP . . . C 3 -19.764 16.815 -9.852 1 22.82 ? C4' ANP 402 A 1 HETATM 16 O O4' ANP . . . C 3 -19.169 16.959 -8.597 1 23.98 ? O4' ANP 402 A 1 HETATM 17 C C3' ANP . . . C 3 -19.056 15.723 -10.558 1 22.87 ? C3' ANP 402 A 1 HETATM 18 O O3' ANP . . . C 3 -18.989 15.991 -11.904 1 24.09 ? O3' ANP 402 A 1 HETATM 19 C C2' ANP . . . C 3 -17.701 15.8 -10.001 1 29.26 ? C2' ANP 402 A 1 HETATM 20 O O2' ANP . . . C 3 -16.899 16.616 -10.768 1 29.27 ? O2' ANP 402 A 1 HETATM 21 C C1' ANP . . . C 3 -17.893 16.403 -8.664 1 26.57 ? C1' ANP 402 A 1 HETATM 22 N N9 ANP . . . C 3 -17.808 15.457 -7.594 1 31.08 ? N9 ANP 402 A 1 HETATM 23 C C8 ANP . . . C 3 -17.549 15.798 -6.319 1 38.92 ? C8 ANP 402 A 1 HETATM 24 N N7 ANP . . . C 3 -17.577 14.741 -5.549 1 36.95 ? N7 ANP 402 A 1 HETATM 25 C C5 ANP . . . C 3 -17.871 13.672 -6.284 1 31.65 ? C5 ANP 402 A 1 HETATM 26 C C6 ANP . . . C 3 -18.028 12.325 -6.011 1 29.33 ? C6 ANP 402 A 1 HETATM 27 N N6 ANP . . . C 3 -17.865 11.822 -4.686 1 35.27 ? N6 ANP 402 A 1 HETATM 28 N N1 ANP . . . C 3 -18.323 11.472 -6.999 1 33.78 ? N1 ANP 402 A 1 HETATM 29 C C2 ANP . . . C 3 -18.48 11.896 -8.268 1 27.61 ? C2 ANP 402 A 1 HETATM 30 N N3 ANP . . . C 3 -18.332 13.201 -8.572 1 25.43 ? N3 ANP 402 A 1 HETATM 31 C C4 ANP . . . C 3 -18.028 14.105 -7.619 1 27.99 ? C4 ANP 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #