data_4JHD # _model_server_result.job_id S4IdvDpVSv3lAVQGGedJNA _model_server_result.datetime_utc '2025-01-13 02:30:40' _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 4jhd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":401}' # _entry.id 4JHD # _exptl.entry_id 4JHD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 65.41 _cell.angle_beta 90.03 _cell.angle_gamma 77.77 _cell.entry_id 4JHD _cell.length_a 53.45 _cell.length_b 99.8 _cell.length_c 118.27 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JHD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,J,O,P,Q 1 1 D,E,F,K,L,M,N,R,S,T 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 G N N ? 4 I N N ? 4 K N N ? 4 M 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 G O1B ANP . A ANP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc2 I O1B ANP . B ANP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc3 I O2G ANP . B ANP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc4 J MG MG . B MG 402 1_555 P O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc5 K O1B ANP . D ANP 401 1_555 L MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc6 L MG MG . D MG 402 1_555 R O HOH . D HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc7 M O1B ANP . E ANP 401 1_555 N MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc8 M O2G ANP . E ANP 401 1_555 N MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc9 N MG MG . E MG 402 1_555 S O HOH . E HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? # _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 4JHD _atom_sites.fract_transf_matrix[1][1] 0.018709 _atom_sites.fract_transf_matrix[1][2] -0.004055 _atom_sites.fract_transf_matrix[1][3] 0.00192 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010253 _atom_sites.fract_transf_matrix[2][3] -0.004826 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009345 _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 G 4 ANP A 1 401 1380 ANP ANP . H 5 MG A 1 402 1 MG MG . I 4 ANP B 1 401 1380 ANP ANP . J 5 MG B 1 402 3 MG MG . K 4 ANP D 1 401 1380 ANP ANP . L 5 MG D 1 402 2 MG MG . M 4 ANP E 1 401 1380 ANP ANP . N 5 MG E 1 402 4 MG MG . O 6 HOH A 1 501 1 HOH HOH . O 6 HOH A 2 502 4 HOH HOH . O 6 HOH A 3 503 12 HOH HOH . O 6 HOH A 4 504 19 HOH HOH . O 6 HOH A 5 505 23 HOH HOH . O 6 HOH A 6 506 28 HOH HOH . O 6 HOH A 7 507 29 HOH HOH . O 6 HOH A 8 508 32 HOH HOH . O 6 HOH A 9 509 35 HOH HOH . O 6 HOH A 10 510 37 HOH HOH . O 6 HOH A 11 511 38 HOH HOH . O 6 HOH A 12 512 42 HOH HOH . O 6 HOH A 13 513 46 HOH HOH . O 6 HOH A 14 514 48 HOH HOH . O 6 HOH A 15 515 52 HOH HOH . O 6 HOH A 16 516 58 HOH HOH . O 6 HOH A 17 517 61 HOH HOH . O 6 HOH A 18 518 65 HOH HOH . O 6 HOH A 19 519 66 HOH HOH . O 6 HOH A 20 520 67 HOH HOH . O 6 HOH A 21 521 69 HOH HOH . O 6 HOH A 22 522 70 HOH HOH . O 6 HOH A 23 523 71 HOH HOH . O 6 HOH A 24 524 72 HOH HOH . O 6 HOH A 25 525 73 HOH HOH . O 6 HOH A 26 526 75 HOH HOH . O 6 HOH A 27 527 77 HOH HOH . O 6 HOH A 28 528 79 HOH HOH . O 6 HOH A 29 529 82 HOH HOH . O 6 HOH A 30 530 87 HOH HOH . O 6 HOH A 31 531 88 HOH HOH . O 6 HOH A 32 532 91 HOH HOH . O 6 HOH A 33 533 93 HOH HOH . O 6 HOH A 34 534 94 HOH HOH . O 6 HOH A 35 535 102 HOH HOH . O 6 HOH A 36 536 104 HOH HOH . O 6 HOH A 37 537 105 HOH HOH . O 6 HOH A 38 538 117 HOH HOH . O 6 HOH A 39 539 129 HOH HOH . O 6 HOH A 40 540 134 HOH HOH . O 6 HOH A 41 541 135 HOH HOH . O 6 HOH A 42 542 139 HOH HOH . O 6 HOH A 43 543 140 HOH HOH . O 6 HOH A 44 544 142 HOH HOH . O 6 HOH A 45 545 145 HOH HOH . O 6 HOH A 46 546 151 HOH HOH . P 6 HOH B 1 501 3 HOH HOH . P 6 HOH B 2 502 15 HOH HOH . P 6 HOH B 3 503 16 HOH HOH . P 6 HOH B 4 504 17 HOH HOH . P 6 HOH B 5 505 27 HOH HOH . P 6 HOH B 6 506 34 HOH HOH . P 6 HOH B 7 507 44 HOH HOH . P 6 HOH B 8 508 45 HOH HOH . P 6 HOH B 9 509 47 HOH HOH . P 6 HOH B 10 510 49 HOH HOH . P 6 HOH B 11 511 53 HOH HOH . P 6 HOH B 12 512 54 HOH HOH . P 6 HOH B 13 513 55 HOH HOH . P 6 HOH B 14 514 57 HOH HOH . P 6 HOH B 15 515 60 HOH HOH . P 6 HOH B 16 516 64 HOH HOH . P 6 HOH B 17 517 68 HOH HOH . P 6 HOH B 18 518 78 HOH HOH . P 6 HOH B 19 519 80 HOH HOH . P 6 HOH B 20 520 83 HOH HOH . P 6 HOH B 21 521 84 HOH HOH . P 6 HOH B 22 522 90 HOH HOH . P 6 HOH B 23 523 96 HOH HOH . P 6 HOH B 24 524 97 HOH HOH . P 6 HOH B 25 525 101 HOH HOH . P 6 HOH B 26 526 106 HOH HOH . P 6 HOH B 27 527 107 HOH HOH . P 6 HOH B 28 528 110 HOH HOH . P 6 HOH B 29 529 114 HOH HOH . P 6 HOH B 30 530 118 HOH HOH . P 6 HOH B 31 531 123 HOH HOH . P 6 HOH B 32 532 125 HOH HOH . P 6 HOH B 33 533 133 HOH HOH . P 6 HOH B 34 534 136 HOH HOH . P 6 HOH B 35 535 137 HOH HOH . P 6 HOH B 36 536 143 HOH HOH . P 6 HOH B 37 537 150 HOH HOH . P 6 HOH B 38 538 154 HOH HOH . P 6 HOH B 39 539 156 HOH HOH . P 6 HOH B 40 540 157 HOH HOH . P 6 HOH B 41 541 159 HOH HOH . P 6 HOH B 42 542 161 HOH HOH . P 6 HOH B 43 543 162 HOH HOH . Q 6 HOH C 1 301 22 HOH HOH . Q 6 HOH C 2 302 43 HOH HOH . Q 6 HOH C 3 303 85 HOH HOH . Q 6 HOH C 4 304 100 HOH HOH . Q 6 HOH C 5 305 103 HOH HOH . Q 6 HOH C 6 306 116 HOH HOH . Q 6 HOH C 7 307 126 HOH HOH . Q 6 HOH C 8 308 127 HOH HOH . Q 6 HOH C 9 309 146 HOH HOH . Q 6 HOH C 10 310 152 HOH HOH . R 6 HOH D 1 501 5 HOH HOH . R 6 HOH D 2 502 6 HOH HOH . R 6 HOH D 3 503 9 HOH HOH . R 6 HOH D 4 504 13 HOH HOH . R 6 HOH D 5 505 14 HOH HOH . R 6 HOH D 6 506 18 HOH HOH . R 6 HOH D 7 507 21 HOH HOH . R 6 HOH D 8 508 24 HOH HOH . R 6 HOH D 9 509 36 HOH HOH . R 6 HOH D 10 510 40 HOH HOH . R 6 HOH D 11 511 41 HOH HOH . R 6 HOH D 12 512 56 HOH HOH . R 6 HOH D 13 513 59 HOH HOH . R 6 HOH D 14 514 62 HOH HOH . R 6 HOH D 15 515 63 HOH HOH . R 6 HOH D 16 516 74 HOH HOH . R 6 HOH D 17 517 86 HOH HOH . R 6 HOH D 18 518 89 HOH HOH . R 6 HOH D 19 519 111 HOH HOH . R 6 HOH D 20 520 119 HOH HOH . R 6 HOH D 21 521 121 HOH HOH . R 6 HOH D 22 522 130 HOH HOH . R 6 HOH D 23 523 131 HOH HOH . R 6 HOH D 24 524 132 HOH HOH . R 6 HOH D 25 525 138 HOH HOH . R 6 HOH D 26 526 141 HOH HOH . R 6 HOH D 27 527 144 HOH HOH . R 6 HOH D 28 528 149 HOH HOH . R 6 HOH D 29 529 153 HOH HOH . R 6 HOH D 30 530 155 HOH HOH . R 6 HOH D 31 531 158 HOH HOH . S 6 HOH E 1 501 8 HOH HOH . S 6 HOH E 2 502 10 HOH HOH . S 6 HOH E 3 503 20 HOH HOH . S 6 HOH E 4 504 25 HOH HOH . S 6 HOH E 5 505 26 HOH HOH . S 6 HOH E 6 506 31 HOH HOH . S 6 HOH E 7 507 33 HOH HOH . S 6 HOH E 8 508 39 HOH HOH . S 6 HOH E 9 509 51 HOH HOH . S 6 HOH E 10 510 76 HOH HOH . S 6 HOH E 11 511 92 HOH HOH . S 6 HOH E 12 512 95 HOH HOH . S 6 HOH E 13 513 108 HOH HOH . S 6 HOH E 14 514 109 HOH HOH . S 6 HOH E 15 515 112 HOH HOH . S 6 HOH E 16 516 113 HOH HOH . S 6 HOH E 17 517 115 HOH HOH . S 6 HOH E 18 518 120 HOH HOH . S 6 HOH E 19 519 122 HOH HOH . S 6 HOH E 20 520 147 HOH HOH . S 6 HOH E 21 521 148 HOH HOH . S 6 HOH E 22 522 160 HOH HOH . T 6 HOH F 1 301 30 HOH HOH . T 6 HOH F 2 302 50 HOH HOH . T 6 HOH F 3 303 81 HOH HOH . T 6 HOH F 4 304 98 HOH HOH . T 6 HOH F 5 305 124 HOH HOH . T 6 HOH F 6 306 128 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 . . . K 4 22.544 -7.664 3.702 1 103.98 ? PG ANP 401 D 1 HETATM 2 O O1G ANP . . . K 4 22.528 -8.657 4.851 1 85.28 ? O1G ANP 401 D 1 HETATM 3 O O2G ANP . . . K 4 22.408 -8.271 2.32 1 81.08 ? O2G ANP 401 D 1 HETATM 4 O O3G ANP . . . K 4 21.631 -6.473 3.907 1 82.29 ? O3G ANP 401 D 1 HETATM 5 P PB ANP . . . K 4 24.959 -6.518 2.284 1 74.37 ? PB ANP 401 D 1 HETATM 6 O O1B ANP . . . K 4 23.975 -6.629 1.139 1 81.61 ? O1B ANP 401 D 1 HETATM 7 O O2B ANP . . . K 4 25.596 -5.173 2.554 1 79.57 ? O2B ANP 401 D 1 HETATM 8 N N3B ANP . . . K 4 24.17 -7.018 3.758 1 79.66 ? N3B ANP 401 D 1 HETATM 9 P PA ANP . . . K 4 26.781 -7.867 0.553 1 84.26 ? PA ANP 401 D 1 HETATM 10 O O1A ANP . . . K 4 25.758 -8.499 -0.371 1 72.3 ? O1A ANP 401 D 1 HETATM 11 O O2A ANP . . . K 4 27.475 -6.596 0.099 1 87.03 ? O2A ANP 401 D 1 HETATM 12 O O3A ANP . . . K 4 26.132 -7.593 2.012 1 80.84 ? O3A ANP 401 D 1 HETATM 13 O O5' ANP . . . K 4 27.892 -8.981 0.941 1 67.54 ? O5' ANP 401 D 1 HETATM 14 C C5' ANP . . . K 4 28.889 -8.698 1.935 1 62.15 ? C5' ANP 401 D 1 HETATM 15 C C4' ANP . . . K 4 29.371 -9.948 2.679 1 63.08 ? C4' ANP 401 D 1 HETATM 16 O O4' ANP . . . K 4 29.885 -10.92 1.765 1 58.99 ? O4' ANP 401 D 1 HETATM 17 C C3' ANP . . . K 4 30.52 -9.608 3.622 1 63.2 ? C3' ANP 401 D 1 HETATM 18 O O3' ANP . . . K 4 30.407 -10.392 4.816 1 65.47 ? O3' ANP 401 D 1 HETATM 19 C C2' ANP . . . K 4 31.777 -9.995 2.869 1 61.03 ? C2' ANP 401 D 1 HETATM 20 O O2' ANP . . . K 4 32.843 -10.396 3.734 1 54.08 ? O2' ANP 401 D 1 HETATM 21 C C1' ANP . . . K 4 31.278 -11.147 2.016 1 60.16 ? C1' ANP 401 D 1 HETATM 22 N N9 ANP . . . K 4 31.961 -11.199 0.71 1 62.96 ? N9 ANP 401 D 1 HETATM 23 C C8 ANP . . . K 4 32.164 -10.17 -0.142 1 57.18 ? C8 ANP 401 D 1 HETATM 24 N N7 ANP . . . K 4 32.811 -10.588 -1.26 1 60.42 ? N7 ANP 401 D 1 HETATM 25 C C5 ANP . . . K 4 33.015 -11.912 -1.118 1 61.46 ? C5 ANP 401 D 1 HETATM 26 C C6 ANP . . . K 4 33.641 -12.982 -1.918 1 58.44 ? C6 ANP 401 D 1 HETATM 27 N N6 ANP . . . K 4 34.16 -12.664 -3.109 1 70.86 ? N6 ANP 401 D 1 HETATM 28 N N1 ANP . . . K 4 33.658 -14.255 -1.442 1 57.4 ? N1 ANP 401 D 1 HETATM 29 C C2 ANP . . . K 4 33.117 -14.546 -0.239 1 59.71 ? C2 ANP 401 D 1 HETATM 30 N N3 ANP . . . K 4 32.53 -13.626 0.562 1 63.86 ? N3 ANP 401 D 1 HETATM 31 C C4 ANP . . . K 4 32.453 -12.317 0.18 1 65.38 ? C4 ANP 401 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #