data_2PMD # _model_server_result.job_id yucjra1w2zaSQRFWl4xOIQ _model_server_result.datetime_utc '2025-04-07 20:18:21' _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 2pmd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":417}' # _entry.id 2PMD # _exptl.entry_id 2PMD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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 2PMD _cell.length_a 95.06 _cell.length_b 95.06 _cell.length_c 165.67 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PMD _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,D,E,F,G,L 1 1 B,H,I,J,K,M 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 # _struct_asym.details ? _struct_asym.entity_id 3 _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 disulf ? disulf1 A SG CYS 59 A CYS 59 1_555 A SG CYS 74 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 62 A CYS 62 1_555 A SG CYS 77 A CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 59 B CYS 59 1_555 B SG CYS 74 B CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 62 B CYS 62 1_555 B SG CYS 77 B CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _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 174 n n PG O2G GNP sing 175 n n PG O3G GNP sing 176 n n PG N3B GNP sing 177 n n O2G HOG2 GNP sing 178 n n O3G HOG3 GNP sing 179 n n N3B PB GNP sing 180 n n N3B HNB3 GNP sing 181 n n PB O1B GNP doub 182 n n PB O2B GNP sing 183 n n PB O3A GNP sing 184 n n O2B HOB2 GNP sing 185 n n O3A PA GNP sing 186 n n PA O1A GNP doub 187 n n PA O2A GNP sing 188 n n PA O5' GNP sing 189 n n O2A HOA2 GNP sing 190 n n O5' C5' GNP sing 191 n n C5' C4' GNP sing 192 n n C5' "H5'2" GNP sing 193 n n C5' "H5'1" GNP sing 194 n n C4' O4' GNP sing 195 n n C4' C3' GNP sing 196 n n C4' H4' GNP sing 197 n n O4' C1' GNP sing 198 n n C3' O3' GNP sing 199 n n C3' C2' GNP sing 200 n n C3' H3' GNP sing 201 n n O3' HO3' GNP sing 202 n n C2' O2' GNP sing 203 n n C2' C1' GNP sing 204 n n C2' H2' GNP sing 205 n n O2' HO2' GNP sing 206 n n C1' N9 GNP sing 207 n n C1' H1' GNP sing 208 n n N9 C8 GNP sing 209 n y N9 C4 GNP sing 210 n y C8 N7 GNP doub 211 n y C8 H8 GNP sing 212 n n N7 C5 GNP sing 213 n y C5 C6 GNP sing 214 n y C5 C4 GNP doub 215 n y C6 O6 GNP doub 216 n n C6 N1 GNP sing 217 n y N1 C2 GNP sing 218 n y N1 HN1 GNP sing 219 n n C2 N2 GNP sing 220 n n C2 N3 GNP doub 221 n y N2 HN21 GNP sing 222 n n N2 HN22 GNP sing 223 n n N3 C4 GNP sing 224 n y # _atom_sites.entry_id 2PMD _atom_sites.fract_transf_matrix[1][1] 0.01052 _atom_sites.fract_transf_matrix[1][2] 0.006074 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012147 _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] 0.006036 _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 GDP A 1 416 201 GDP GDP . D 3 GNP A 1 417 203 GNP GNP . E 4 PPV A 1 418 205 PPV PPV . F 4 PPV A 1 419 206 PPV PPV . G 4 PPV A 1 420 209 PPV PPV . H 2 GDP B 1 416 202 GDP GDP . I 4 PPV B 1 417 204 PPV PPV . J 4 PPV B 1 418 207 PPV PPV . K 4 PPV B 1 419 208 PPV PPV . L 5 HOH A 1 421 0 HOH HOH . L 5 HOH A 2 422 1 HOH HOH . L 5 HOH A 3 423 4 HOH HOH . L 5 HOH A 4 424 6 HOH HOH . L 5 HOH A 5 425 8 HOH HOH . L 5 HOH A 6 426 9 HOH HOH . L 5 HOH A 7 427 10 HOH HOH . L 5 HOH A 8 428 12 HOH HOH . L 5 HOH A 9 429 17 HOH HOH . L 5 HOH A 10 430 20 HOH HOH . L 5 HOH A 11 431 24 HOH HOH . L 5 HOH A 12 432 29 HOH HOH . L 5 HOH A 13 433 30 HOH HOH . L 5 HOH A 14 434 37 HOH HOH . L 5 HOH A 15 435 39 HOH HOH . L 5 HOH A 16 436 42 HOH HOH . L 5 HOH A 17 437 43 HOH HOH . L 5 HOH A 18 438 47 HOH HOH . L 5 HOH A 19 439 51 HOH HOH . L 5 HOH A 20 440 53 HOH HOH . L 5 HOH A 21 441 54 HOH HOH . L 5 HOH A 22 442 58 HOH HOH . L 5 HOH A 23 443 59 HOH HOH . L 5 HOH A 24 444 60 HOH HOH . L 5 HOH A 25 445 61 HOH HOH . L 5 HOH A 26 446 62 HOH HOH . L 5 HOH A 27 447 65 HOH HOH . L 5 HOH A 28 448 66 HOH HOH . L 5 HOH A 29 449 67 HOH HOH . L 5 HOH A 30 450 69 HOH HOH . L 5 HOH A 31 451 73 HOH HOH . L 5 HOH A 32 452 74 HOH HOH . L 5 HOH A 33 453 77 HOH HOH . L 5 HOH A 34 454 80 HOH HOH . L 5 HOH A 35 455 81 HOH HOH . L 5 HOH A 36 456 83 HOH HOH . L 5 HOH A 37 457 85 HOH HOH . L 5 HOH A 38 458 89 HOH HOH . L 5 HOH A 39 459 90 HOH HOH . L 5 HOH A 40 460 91 HOH HOH . L 5 HOH A 41 461 99 HOH HOH . L 5 HOH A 42 462 101 HOH HOH . L 5 HOH A 43 463 102 HOH HOH . L 5 HOH A 44 464 103 HOH HOH . L 5 HOH A 45 465 109 HOH HOH . L 5 HOH A 46 466 116 HOH HOH . L 5 HOH A 47 467 117 HOH HOH . L 5 HOH A 48 468 119 HOH HOH . L 5 HOH A 49 469 120 HOH HOH . L 5 HOH A 50 470 123 HOH HOH . L 5 HOH A 51 471 125 HOH HOH . L 5 HOH A 52 472 128 HOH HOH . L 5 HOH A 53 473 129 HOH HOH . L 5 HOH A 54 474 130 HOH HOH . L 5 HOH A 55 475 132 HOH HOH . L 5 HOH A 56 476 134 HOH HOH . L 5 HOH A 57 477 137 HOH HOH . L 5 HOH A 58 478 139 HOH HOH . L 5 HOH A 59 479 143 HOH HOH . L 5 HOH A 60 480 145 HOH HOH . L 5 HOH A 61 481 148 HOH HOH . L 5 HOH A 62 482 150 HOH HOH . L 5 HOH A 63 483 151 HOH HOH . L 5 HOH A 64 484 154 HOH HOH . L 5 HOH A 65 485 156 HOH HOH . L 5 HOH A 66 486 157 HOH HOH . L 5 HOH A 67 487 160 HOH HOH . L 5 HOH A 68 488 164 HOH HOH . L 5 HOH A 69 489 166 HOH HOH . L 5 HOH A 70 490 170 HOH HOH . L 5 HOH A 71 491 172 HOH HOH . M 5 HOH B 1 420 2 HOH HOH . M 5 HOH B 2 421 3 HOH HOH . M 5 HOH B 3 422 5 HOH HOH . M 5 HOH B 4 423 7 HOH HOH . M 5 HOH B 5 424 11 HOH HOH . M 5 HOH B 6 425 14 HOH HOH . M 5 HOH B 7 426 15 HOH HOH . M 5 HOH B 8 427 16 HOH HOH . M 5 HOH B 9 428 18 HOH HOH . M 5 HOH B 10 429 19 HOH HOH . M 5 HOH B 11 430 21 HOH HOH . M 5 HOH B 12 431 22 HOH HOH . M 5 HOH B 13 432 23 HOH HOH . M 5 HOH B 14 433 25 HOH HOH . M 5 HOH B 15 434 26 HOH HOH . M 5 HOH B 16 435 27 HOH HOH . M 5 HOH B 17 436 28 HOH HOH . M 5 HOH B 18 437 31 HOH HOH . M 5 HOH B 19 438 32 HOH HOH . M 5 HOH B 20 439 33 HOH HOH . M 5 HOH B 21 440 34 HOH HOH . M 5 HOH B 22 441 35 HOH HOH . M 5 HOH B 23 442 36 HOH HOH . M 5 HOH B 24 443 38 HOH HOH . M 5 HOH B 25 444 40 HOH HOH . M 5 HOH B 26 445 41 HOH HOH . M 5 HOH B 27 446 44 HOH HOH . M 5 HOH B 28 447 45 HOH HOH . M 5 HOH B 29 448 46 HOH HOH . M 5 HOH B 30 449 48 HOH HOH . M 5 HOH B 31 450 49 HOH HOH . M 5 HOH B 32 451 50 HOH HOH . M 5 HOH B 33 452 52 HOH HOH . M 5 HOH B 34 453 55 HOH HOH . M 5 HOH B 35 454 56 HOH HOH . M 5 HOH B 36 455 57 HOH HOH . M 5 HOH B 37 456 68 HOH HOH . M 5 HOH B 38 457 70 HOH HOH . M 5 HOH B 39 458 71 HOH HOH . M 5 HOH B 40 459 75 HOH HOH . M 5 HOH B 41 460 78 HOH HOH . M 5 HOH B 42 461 82 HOH HOH . M 5 HOH B 43 462 84 HOH HOH . M 5 HOH B 44 463 87 HOH HOH . M 5 HOH B 45 464 88 HOH HOH . M 5 HOH B 46 465 92 HOH HOH . M 5 HOH B 47 466 93 HOH HOH . M 5 HOH B 48 467 94 HOH HOH . M 5 HOH B 49 468 95 HOH HOH . M 5 HOH B 50 469 96 HOH HOH . M 5 HOH B 51 470 97 HOH HOH . M 5 HOH B 52 471 98 HOH HOH . M 5 HOH B 53 472 100 HOH HOH . M 5 HOH B 54 473 104 HOH HOH . M 5 HOH B 55 474 105 HOH HOH . M 5 HOH B 56 475 106 HOH HOH . M 5 HOH B 57 476 107 HOH HOH . M 5 HOH B 58 477 112 HOH HOH . M 5 HOH B 59 478 113 HOH HOH . M 5 HOH B 60 479 114 HOH HOH . M 5 HOH B 61 480 115 HOH HOH . M 5 HOH B 62 481 118 HOH HOH . M 5 HOH B 63 482 121 HOH HOH . M 5 HOH B 64 483 122 HOH HOH . M 5 HOH B 65 484 126 HOH HOH . M 5 HOH B 66 485 127 HOH HOH . M 5 HOH B 67 486 131 HOH HOH . M 5 HOH B 68 487 135 HOH HOH . M 5 HOH B 69 488 138 HOH HOH . M 5 HOH B 70 489 140 HOH HOH . M 5 HOH B 71 490 141 HOH HOH . M 5 HOH B 72 491 142 HOH HOH . M 5 HOH B 73 492 144 HOH HOH . M 5 HOH B 74 493 147 HOH HOH . M 5 HOH B 75 494 149 HOH HOH . M 5 HOH B 76 495 152 HOH HOH . M 5 HOH B 77 496 153 HOH HOH . M 5 HOH B 78 497 155 HOH HOH . M 5 HOH B 79 498 158 HOH HOH . M 5 HOH B 80 499 159 HOH HOH . M 5 HOH B 81 500 161 HOH HOH . M 5 HOH B 82 501 162 HOH HOH . M 5 HOH B 83 502 163 HOH HOH . M 5 HOH B 84 503 165 HOH HOH . M 5 HOH B 85 504 167 HOH HOH . M 5 HOH B 86 505 168 HOH HOH . M 5 HOH B 87 506 169 HOH HOH . M 5 HOH B 88 507 171 HOH HOH . M 5 HOH B 89 508 173 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 GNP . . . D 3 27.681 -1.861 -2.163 0.97 21.68 ? PG GNP 417 A 1 HETATM 2 O O1G GNP . . . D 3 29.017 -1.201 -2.693 1 22.18 ? O1G GNP 417 A 1 HETATM 3 O O2G GNP . . . D 3 27.966 -2.537 -0.612 1 19.99 ? O2G GNP 417 A 1 HETATM 4 O O3G GNP . . . D 3 27.163 -3.079 -3.251 1 23.33 ? O3G GNP 417 A 1 HETATM 5 N N3B GNP . . . D 3 26.473 -0.619 -2.031 1 19.12 ? N3B GNP 417 A 1 HETATM 6 P PB GNP . . . D 3 26.2 0.057 -3.602 0.98 17.18 ? PB GNP 417 A 1 HETATM 7 O O1B GNP . . . D 3 27.569 0.686 -4.173 1 16.88 ? O1B GNP 417 A 1 HETATM 8 O O2B GNP . . . D 3 25.635 -1.184 -4.633 0.98 17.04 ? O2B GNP 417 A 1 HETATM 9 O O3A GNP . . . D 3 25.024 1.299 -3.478 0.93 16.72 ? O3A GNP 417 A 1 HETATM 10 P PA GNP . . . D 3 24.6 2.058 -4.882 1 168.31 ? PA GNP 417 A 1 HETATM 11 O O1A GNP . . . D 3 25.771 2.714 -5.524 1 168.06 ? O1A GNP 417 A 1 HETATM 12 O O2A GNP . . . D 3 23.945 1.022 -5.935 1 168.32 ? O2A GNP 417 A 1 HETATM 13 O O5' GNP . . . D 3 23.55 3.175 -4.406 1 166.19 ? O5' GNP 417 A 1 HETATM 14 C C5' GNP . . . D 3 23.048 3.957 -5.477 1 162.5 ? C5' GNP 417 A 1 HETATM 15 C C4' GNP . . . D 3 22.186 4.998 -4.771 1 160.44 ? C4' GNP 417 A 1 HETATM 16 O O4' GNP . . . D 3 23.017 5.745 -3.869 1 159.01 ? O4' GNP 417 A 1 HETATM 17 C C3' GNP . . . D 3 21.516 5.972 -5.744 1 159.65 ? C3' GNP 417 A 1 HETATM 18 O O3' GNP . . . D 3 20.212 5.52 -6.081 1 160.6 ? O3' GNP 417 A 1 HETATM 19 C C2' GNP . . . D 3 21.601 7.326 -4.994 1 158.56 ? C2' GNP 417 A 1 HETATM 20 O O2' GNP . . . D 3 20.351 7.987 -4.739 1 156.83 ? O2' GNP 417 A 1 HETATM 21 C C1' GNP . . . D 3 22.341 7.001 -3.667 1 157.88 ? C1' GNP 417 A 1 HETATM 22 N N9 GNP . . . D 3 23.307 8.073 -3.322 1 156.86 ? N9 GNP 417 A 1 HETATM 23 C C8 GNP . . . D 3 24.623 8.101 -3.729 1 156.34 ? C8 GNP 417 A 1 HETATM 24 N N7 GNP . . . D 3 25.221 9.153 -3.277 1 156.11 ? N7 GNP 417 A 1 HETATM 25 C C5 GNP . . . D 3 24.342 9.882 -2.545 1 156.2 ? C5 GNP 417 A 1 HETATM 26 C C6 GNP . . . D 3 24.431 11.107 -1.822 1 156.09 ? C6 GNP 417 A 1 HETATM 27 O O6 GNP . . . D 3 25.483 11.729 -1.783 1 155.84 ? O6 GNP 417 A 1 HETATM 28 N N1 GNP . . . D 3 23.314 11.571 -1.174 1 155.88 ? N1 GNP 417 A 1 HETATM 29 C C2 GNP . . . D 3 22.125 10.872 -1.216 1 155.56 ? C2 GNP 417 A 1 HETATM 30 N N2 GNP . . . D 3 21.034 11.373 -0.554 1 154.83 ? N2 GNP 417 A 1 HETATM 31 N N3 GNP . . . D 3 22.025 9.723 -1.89 1 155.89 ? N3 GNP 417 A 1 HETATM 32 C C4 GNP . . . D 3 23.095 9.199 -2.56 1 156.29 ? C4 GNP 417 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #