data_1ZC4 # _model_server_result.job_id RbxuIVBHXoo97qfrBQiX_A _model_server_result.datetime_utc '2024-11-24 09:18:17' _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 1zc4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":500}' # _entry.id 1ZC4 # _exptl.entry_id 1ZC4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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 102.77 _cell.angle_gamma 90 _cell.entry_id 1ZC4 _cell.length_a 52.912 _cell.length_b 113.389 _cell.length_c 70.68 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZC4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,I,L 1 1 B,C,G,H,J,K 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 F N N ? 4 H 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 20 A SER 28 1_555 E MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc2 A OG1 THR 38 A THR 46 1_555 E MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc3 E MG MG . A MG 200 1_555 F O2G GNP . A GNP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc4 E MG MG . A MG 200 1_555 F O2B GNP . A GNP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc5 E MG MG . A MG 200 1_555 I O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc6 E MG MG . A MG 200 1_555 I O HOH . A HOH 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc7 C OG SER 20 C SER 28 1_555 G MG MG . C MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc8 C OG1 THR 38 C THR 46 1_555 G MG MG . C MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc9 G MG MG . C MG 300 1_555 H O2G GNP . C GNP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc10 G MG MG . C MG 300 1_555 H O2B GNP . C GNP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc11 G MG MG . C MG 300 1_555 K O HOH . C HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc12 G MG MG . C MG 300 1_555 K O HOH . C HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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 GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 1ZC4 _atom_sites.fract_transf_matrix[1][1] 0.018899 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004285 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008819 _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] 0.014507 _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 E 3 MG A 1 200 200 MG MG . F 4 GNP A 1 400 400 GNP GNP . G 3 MG C 1 300 300 MG MG . H 4 GNP C 1 500 500 GNP GNP . I 5 HOH A 1 401 5 HOH WAT . I 5 HOH A 2 402 7 HOH WAT . I 5 HOH A 3 403 9 HOH WAT . I 5 HOH A 4 404 15 HOH WAT . I 5 HOH A 5 405 16 HOH WAT . I 5 HOH A 6 406 18 HOH WAT . I 5 HOH A 7 407 19 HOH WAT . I 5 HOH A 8 408 25 HOH WAT . I 5 HOH A 9 409 26 HOH WAT . I 5 HOH A 10 410 38 HOH WAT . I 5 HOH A 11 411 40 HOH WAT . I 5 HOH A 12 412 44 HOH WAT . I 5 HOH A 13 413 46 HOH WAT . I 5 HOH A 14 414 51 HOH WAT . I 5 HOH A 15 415 56 HOH WAT . I 5 HOH A 16 416 68 HOH WAT . I 5 HOH A 17 417 69 HOH WAT . I 5 HOH A 18 418 73 HOH WAT . I 5 HOH A 19 419 74 HOH WAT . I 5 HOH A 20 420 79 HOH WAT . I 5 HOH A 21 421 87 HOH WAT . I 5 HOH A 22 422 90 HOH WAT . I 5 HOH A 23 423 92 HOH WAT . I 5 HOH A 24 424 94 HOH WAT . I 5 HOH A 25 425 97 HOH WAT . I 5 HOH A 26 426 99 HOH WAT . I 5 HOH A 27 427 108 HOH WAT . I 5 HOH A 28 428 110 HOH WAT . I 5 HOH A 29 429 111 HOH WAT . I 5 HOH A 30 430 116 HOH WAT . I 5 HOH A 31 431 118 HOH WAT . I 5 HOH A 32 432 124 HOH WAT . I 5 HOH A 33 433 125 HOH WAT . I 5 HOH A 34 434 127 HOH WAT . I 5 HOH A 35 435 128 HOH WAT . I 5 HOH A 36 436 131 HOH WAT . I 5 HOH A 37 437 133 HOH WAT . I 5 HOH A 38 438 136 HOH WAT . I 5 HOH A 39 439 139 HOH WAT . I 5 HOH A 40 440 140 HOH WAT . I 5 HOH A 41 441 146 HOH WAT . I 5 HOH A 42 442 147 HOH WAT . I 5 HOH A 43 443 148 HOH WAT . I 5 HOH A 44 444 153 HOH WAT . J 5 HOH B 1 2 2 HOH WAT . J 5 HOH B 2 6 6 HOH WAT . J 5 HOH B 3 13 13 HOH WAT . J 5 HOH B 4 14 14 HOH WAT . J 5 HOH B 5 17 17 HOH WAT . J 5 HOH B 6 22 22 HOH WAT . J 5 HOH B 7 23 23 HOH WAT . J 5 HOH B 8 33 33 HOH WAT . J 5 HOH B 9 34 34 HOH WAT . J 5 HOH B 10 35 35 HOH WAT . J 5 HOH B 11 50 50 HOH WAT . J 5 HOH B 12 53 53 HOH WAT . J 5 HOH B 13 60 60 HOH WAT . J 5 HOH B 14 61 61 HOH WAT . J 5 HOH B 15 65 65 HOH WAT . J 5 HOH B 16 67 67 HOH WAT . J 5 HOH B 17 70 70 HOH WAT . J 5 HOH B 18 71 71 HOH WAT . J 5 HOH B 19 78 78 HOH WAT . J 5 HOH B 20 89 89 HOH WAT . J 5 HOH B 21 95 95 HOH WAT . J 5 HOH B 22 102 102 HOH WAT . J 5 HOH B 23 103 103 HOH WAT . J 5 HOH B 24 117 117 HOH WAT . J 5 HOH B 25 119 119 HOH WAT . J 5 HOH B 26 126 126 HOH WAT . J 5 HOH B 27 130 130 HOH WAT . J 5 HOH B 28 135 135 HOH WAT . J 5 HOH B 29 137 137 HOH WAT . J 5 HOH B 30 143 143 HOH WAT . J 5 HOH B 31 144 144 HOH WAT . K 5 HOH C 1 501 3 HOH WAT . K 5 HOH C 2 502 4 HOH WAT . K 5 HOH C 3 503 10 HOH WAT . K 5 HOH C 4 504 11 HOH WAT . K 5 HOH C 5 505 12 HOH WAT . K 5 HOH C 6 506 21 HOH WAT . K 5 HOH C 7 507 24 HOH WAT . K 5 HOH C 8 508 27 HOH WAT . K 5 HOH C 9 509 28 HOH WAT . K 5 HOH C 10 510 32 HOH WAT . K 5 HOH C 11 511 37 HOH WAT . K 5 HOH C 12 512 39 HOH WAT . K 5 HOH C 13 513 42 HOH WAT . K 5 HOH C 14 514 47 HOH WAT . K 5 HOH C 15 515 55 HOH WAT . K 5 HOH C 16 516 58 HOH WAT . K 5 HOH C 17 517 59 HOH WAT . K 5 HOH C 18 518 62 HOH WAT . K 5 HOH C 19 519 63 HOH WAT . K 5 HOH C 20 520 66 HOH WAT . K 5 HOH C 21 521 72 HOH WAT . K 5 HOH C 22 522 76 HOH WAT . K 5 HOH C 23 523 77 HOH WAT . K 5 HOH C 24 524 80 HOH WAT . K 5 HOH C 25 525 81 HOH WAT . K 5 HOH C 26 526 82 HOH WAT . K 5 HOH C 27 527 83 HOH WAT . K 5 HOH C 28 528 85 HOH WAT . K 5 HOH C 29 529 86 HOH WAT . K 5 HOH C 30 530 88 HOH WAT . K 5 HOH C 31 531 91 HOH WAT . K 5 HOH C 32 532 93 HOH WAT . K 5 HOH C 33 533 98 HOH WAT . K 5 HOH C 34 534 100 HOH WAT . K 5 HOH C 35 535 104 HOH WAT . K 5 HOH C 36 536 106 HOH WAT . K 5 HOH C 37 537 107 HOH WAT . K 5 HOH C 38 538 109 HOH WAT . K 5 HOH C 39 539 113 HOH WAT . K 5 HOH C 40 540 115 HOH WAT . K 5 HOH C 41 541 122 HOH WAT . K 5 HOH C 42 542 123 HOH WAT . K 5 HOH C 43 543 132 HOH WAT . K 5 HOH C 44 544 134 HOH WAT . K 5 HOH C 45 545 138 HOH WAT . K 5 HOH C 46 546 145 HOH WAT . K 5 HOH C 47 547 149 HOH WAT . K 5 HOH C 48 548 150 HOH WAT . K 5 HOH C 49 549 151 HOH WAT . K 5 HOH C 50 550 152 HOH WAT . L 5 HOH D 1 1 1 HOH WAT . L 5 HOH D 2 8 8 HOH WAT . L 5 HOH D 3 20 20 HOH WAT . L 5 HOH D 4 29 29 HOH WAT . L 5 HOH D 5 30 30 HOH WAT . L 5 HOH D 6 31 31 HOH WAT . L 5 HOH D 7 36 36 HOH WAT . L 5 HOH D 8 41 41 HOH WAT . L 5 HOH D 9 43 43 HOH WAT . L 5 HOH D 10 45 45 HOH WAT . L 5 HOH D 11 48 48 HOH WAT . L 5 HOH D 12 49 49 HOH WAT . L 5 HOH D 13 52 52 HOH WAT . L 5 HOH D 14 54 54 HOH WAT . L 5 HOH D 15 57 57 HOH WAT . L 5 HOH D 16 64 64 HOH WAT . L 5 HOH D 17 75 75 HOH WAT . L 5 HOH D 18 84 84 HOH WAT . L 5 HOH D 19 96 96 HOH WAT . L 5 HOH D 20 101 101 HOH WAT . L 5 HOH D 21 105 105 HOH WAT . L 5 HOH D 22 112 112 HOH WAT . L 5 HOH D 23 114 114 HOH WAT . L 5 HOH D 24 120 120 HOH WAT . L 5 HOH D 25 121 121 HOH WAT . L 5 HOH D 26 129 129 HOH WAT . L 5 HOH D 27 141 141 HOH WAT . L 5 HOH D 28 142 142 HOH WAT . # 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 GNP . . . H 4 6.523 22.249 14.65 1 31.52 ? PG GNP 500 C 1 HETATM 2 O O1G GNP . . . H 4 6.441 23.519 13.844 1 31.28 ? O1G GNP 500 C 1 HETATM 3 O O2G GNP . . . H 4 6.671 22.523 16.134 1 29.3 ? O2G GNP 500 C 1 HETATM 4 O O3G GNP . . . H 4 7.627 21.392 14.128 1 27.2 ? O3G GNP 500 C 1 HETATM 5 N N3B GNP . . . H 4 5.04 21.441 14.457 1 28.22 ? N3B GNP 500 C 1 HETATM 6 P PB GNP . . . H 4 4.684 19.996 15.2 1 28.74 ? PB GNP 500 C 1 HETATM 7 O O1B GNP . . . H 4 5.285 18.818 14.558 1 30.14 ? O1B GNP 500 C 1 HETATM 8 O O2B GNP . . . H 4 5.004 20.147 16.686 1 28.93 ? O2B GNP 500 C 1 HETATM 9 O O3A GNP . . . H 4 3.107 19.862 14.976 1 30.06 ? O3A GNP 500 C 1 HETATM 10 P PA GNP . . . H 4 1.932 20.204 16.033 1 27.73 ? PA GNP 500 C 1 HETATM 11 O O1A GNP . . . H 4 1.933 19.255 17.2 1 32.23 ? O1A GNP 500 C 1 HETATM 12 O O2A GNP . . . H 4 2.072 21.664 16.325 1 28.43 ? O2A GNP 500 C 1 HETATM 13 O O5' GNP . . . H 4 0.682 19.864 15.125 1 31.89 ? O5' GNP 500 C 1 HETATM 14 C C5' GNP . . . H 4 0.423 20.617 13.906 1 34 ? C5' GNP 500 C 1 HETATM 15 C C4' GNP . . . H 4 -1.056 20.659 13.618 1 36.71 ? C4' GNP 500 C 1 HETATM 16 O O4' GNP . . . H 4 -1.511 19.281 13.373 1 36.83 ? O4' GNP 500 C 1 HETATM 17 C C3' GNP . . . H 4 -1.944 21.188 14.756 1 33.94 ? C3' GNP 500 C 1 HETATM 18 O O3' GNP . . . H 4 -2.989 21.973 14.129 1 36.97 ? O3' GNP 500 C 1 HETATM 19 C C2' GNP . . . H 4 -2.503 19.954 15.395 1 35.03 ? C2' GNP 500 C 1 HETATM 20 O O2' GNP . . . H 4 -3.763 20.081 16.048 1 37.8 ? O2' GNP 500 C 1 HETATM 21 C C1' GNP . . . H 4 -2.59 18.942 14.253 1 33.37 ? C1' GNP 500 C 1 HETATM 22 N N9 GNP . . . H 4 -2.398 17.577 14.669 1 35.33 ? N9 GNP 500 C 1 HETATM 23 C C8 GNP . . . H 4 -1.311 17.001 15.276 1 34.07 ? C8 GNP 500 C 1 HETATM 24 N N7 GNP . . . H 4 -1.438 15.72 15.531 1 35.35 ? N7 GNP 500 C 1 HETATM 25 C C5 GNP . . . H 4 -2.707 15.442 15.053 1 36.41 ? C5 GNP 500 C 1 HETATM 26 C C6 GNP . . . H 4 -3.42 14.195 15.045 1 34.71 ? C6 GNP 500 C 1 HETATM 27 O O6 GNP . . . H 4 -3.079 13.099 15.453 1 37.04 ? O6 GNP 500 C 1 HETATM 28 N N1 GNP . . . H 4 -4.709 14.327 14.46 1 34.15 ? N1 GNP 500 C 1 HETATM 29 C C2 GNP . . . H 4 -5.24 15.498 13.952 1 34.45 ? C2 GNP 500 C 1 HETATM 30 N N2 GNP . . . H 4 -6.487 15.427 13.436 1 34.25 ? N2 GNP 500 C 1 HETATM 31 N N3 GNP . . . H 4 -4.565 16.659 13.961 1 33.09 ? N3 GNP 500 C 1 HETATM 32 C C4 GNP . . . H 4 -3.306 16.555 14.527 1 37.87 ? C4 GNP 500 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #