data_9LPD # _model_server_result.job_id CSQBMLOQFyyDITBSubfQXw _model_server_result.datetime_utc '2025-07-14 16:30:37' _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 9lpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 9LPD # _exptl.entry_id 9LPD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 533.431 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "TRYPTOPHANYL-5'AMP" _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 105.71 _cell.angle_gamma 90 _cell.entry_id 9LPD _cell.length_a 61.773 _cell.length_b 79.435 _cell.length_c 79.278 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9LPD _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 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,F,G,H,I,J _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 5 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H24 N7 O8 P' _chem_comp.formula_weight 533.431 _chem_comp.id TYM _chem_comp.mon_nstd_flag . _chem_comp.name "TRYPTOPHANYL-5'AMP" _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 P O1P TYM sing 414 n n P O2P TYM doub 415 n n P O5' TYM sing 416 n n P OPP TYM sing 417 n n O1P H1PO TYM sing 418 n n O5' C5' TYM sing 419 n n C5' C4' TYM sing 420 n n C5' "H5'1" TYM sing 421 n n C5' "H5'2" TYM sing 422 n n C4' O4' TYM sing 423 n n C4' C3' TYM sing 424 n n C4' "H4'C" TYM sing 425 n n O4' C1' TYM sing 426 n n C1' N9 TYM sing 427 n n C1' C2' TYM sing 428 n n C1' "H1'C" TYM sing 429 n n N9 C4 TYM sing 430 n y N9 C8 TYM sing 431 n y C4 N3 TYM doub 432 n y C4 C5 TYM sing 433 n y N3 C2 TYM sing 434 n y C2 N1 TYM doub 435 n y C2 HC2 TYM sing 436 n n N1 C6 TYM sing 437 n y C6 N6 TYM sing 438 n n C6 C5 TYM doub 439 n y N6 HN61 TYM sing 440 n n N6 HN62 TYM sing 441 n n C5 N7 TYM sing 442 n y N7 C8 TYM doub 443 n y C8 HC8 TYM sing 444 n n C2' O2' TYM sing 445 n n C2' C3' TYM sing 446 n n C2' "H2'C" TYM sing 447 n n O2' "H2'O" TYM sing 448 n n C3' O3' TYM sing 449 n n C3' "H3'C" TYM sing 450 n n O3' "H3'O" TYM sing 451 n n NH3 CA TYM sing 452 n n NH3 HH31 TYM sing 453 n n NH3 HH32 TYM sing 454 n n CA CB TYM sing 455 n n CA C TYM sing 456 n n CA HCA TYM sing 457 n n CB CG TYM sing 458 n n CB HCB1 TYM sing 459 n n CB HCB2 TYM sing 460 n n CG CD2 TYM sing 461 n y CG CD1 TYM doub 462 n y CD2 CE2 TYM doub 463 n y CD2 CE3 TYM sing 464 n y CE2 NE1 TYM sing 465 n y CE2 CZ2 TYM sing 466 n y CE3 CZ3 TYM doub 467 n y CE3 HE3C TYM sing 468 n n CD1 NE1 TYM sing 469 n y CD1 HD1C TYM sing 470 n n NE1 HE1N TYM sing 471 n n CZ2 CH2 TYM doub 472 n y CZ2 HZ2C TYM sing 473 n n CZ3 CH2 TYM sing 474 n y CZ3 HZ3C TYM sing 475 n n CH2 HH2C TYM sing 476 n n C O TYM doub 477 n n C OPP TYM sing 478 n n # _atom_sites.entry_id 9LPD _atom_sites.fract_transf_matrix[1][1] 0.016188 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004554 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012589 _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] 0.013104 _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 A1EK0 A 1 401 401 A1EK0 TRB . D 3 SO4 A 1 402 1 SO4 SO4 . E 3 SO4 A 1 403 2 SO4 SO4 . F 4 CLW B 1 401 402 CLW Chl . G 5 TYM B 1 402 403 TYM LIG . H 3 SO4 B 1 403 3 SO4 SO4 . I 6 HOH A 1 501 36 HOH HOH . I 6 HOH A 2 502 70 HOH HOH . I 6 HOH A 3 503 3 HOH HOH . I 6 HOH A 4 504 41 HOH HOH . I 6 HOH A 5 505 91 HOH HOH . I 6 HOH A 6 506 127 HOH HOH . I 6 HOH A 7 507 89 HOH HOH . I 6 HOH A 8 508 92 HOH HOH . I 6 HOH A 9 509 145 HOH HOH . I 6 HOH A 10 510 166 HOH HOH . I 6 HOH A 11 511 32 HOH HOH . I 6 HOH A 12 512 120 HOH HOH . I 6 HOH A 13 513 79 HOH HOH . I 6 HOH A 14 514 1 HOH HOH . I 6 HOH A 15 515 117 HOH HOH . I 6 HOH A 16 516 93 HOH HOH . I 6 HOH A 17 517 65 HOH HOH . I 6 HOH A 18 518 46 HOH HOH . I 6 HOH A 19 519 22 HOH HOH . I 6 HOH A 20 520 151 HOH HOH . I 6 HOH A 21 521 8 HOH HOH . I 6 HOH A 22 522 194 HOH HOH . I 6 HOH A 23 523 44 HOH HOH . I 6 HOH A 24 524 87 HOH HOH . I 6 HOH A 25 525 196 HOH HOH . I 6 HOH A 26 526 7 HOH HOH . I 6 HOH A 27 527 195 HOH HOH . I 6 HOH A 28 528 26 HOH HOH . I 6 HOH A 29 529 133 HOH HOH . I 6 HOH A 30 530 206 HOH HOH . I 6 HOH A 31 531 28 HOH HOH . I 6 HOH A 32 532 5 HOH HOH . I 6 HOH A 33 533 139 HOH HOH . I 6 HOH A 34 534 9 HOH HOH . I 6 HOH A 35 535 164 HOH HOH . I 6 HOH A 36 536 150 HOH HOH . I 6 HOH A 37 537 66 HOH HOH . I 6 HOH A 38 538 29 HOH HOH . I 6 HOH A 39 539 171 HOH HOH . I 6 HOH A 40 540 45 HOH HOH . I 6 HOH A 41 541 99 HOH HOH . I 6 HOH A 42 542 96 HOH HOH . I 6 HOH A 43 543 86 HOH HOH . I 6 HOH A 44 544 81 HOH HOH . I 6 HOH A 45 545 23 HOH HOH . I 6 HOH A 46 546 115 HOH HOH . I 6 HOH A 47 547 14 HOH HOH . I 6 HOH A 48 548 147 HOH HOH . I 6 HOH A 49 549 37 HOH HOH . I 6 HOH A 50 550 2 HOH HOH . I 6 HOH A 51 551 176 HOH HOH . I 6 HOH A 52 552 57 HOH HOH . I 6 HOH A 53 553 75 HOH HOH . I 6 HOH A 54 554 146 HOH HOH . I 6 HOH A 55 555 42 HOH HOH . I 6 HOH A 56 556 33 HOH HOH . I 6 HOH A 57 557 51 HOH HOH . I 6 HOH A 58 558 11 HOH HOH . I 6 HOH A 59 559 188 HOH HOH . I 6 HOH A 60 560 106 HOH HOH . I 6 HOH A 61 561 76 HOH HOH . I 6 HOH A 62 562 128 HOH HOH . I 6 HOH A 63 563 213 HOH HOH . I 6 HOH A 64 564 43 HOH HOH . I 6 HOH A 65 565 72 HOH HOH . I 6 HOH A 66 566 202 HOH HOH . I 6 HOH A 67 567 209 HOH HOH . I 6 HOH A 68 568 212 HOH HOH . I 6 HOH A 69 569 114 HOH HOH . I 6 HOH A 70 570 105 HOH HOH . I 6 HOH A 71 571 123 HOH HOH . I 6 HOH A 72 572 83 HOH HOH . I 6 HOH A 73 573 100 HOH HOH . I 6 HOH A 74 574 205 HOH HOH . I 6 HOH A 75 575 152 HOH HOH . I 6 HOH A 76 576 102 HOH HOH . I 6 HOH A 77 577 67 HOH HOH . I 6 HOH A 78 578 27 HOH HOH . I 6 HOH A 79 579 129 HOH HOH . I 6 HOH A 80 580 107 HOH HOH . I 6 HOH A 81 581 55 HOH HOH . I 6 HOH A 82 582 54 HOH HOH . I 6 HOH A 83 583 103 HOH HOH . I 6 HOH A 84 584 153 HOH HOH . I 6 HOH A 85 585 192 HOH HOH . I 6 HOH A 86 586 211 HOH HOH . I 6 HOH A 87 587 90 HOH HOH . I 6 HOH A 88 588 58 HOH HOH . I 6 HOH A 89 589 170 HOH HOH . I 6 HOH A 90 590 124 HOH HOH . I 6 HOH A 91 591 183 HOH HOH . J 6 HOH B 1 501 71 HOH HOH . J 6 HOH B 2 502 48 HOH HOH . J 6 HOH B 3 503 17 HOH HOH . J 6 HOH B 4 504 135 HOH HOH . J 6 HOH B 5 505 130 HOH HOH . J 6 HOH B 6 506 111 HOH HOH . J 6 HOH B 7 507 69 HOH HOH . J 6 HOH B 8 508 12 HOH HOH . J 6 HOH B 9 509 98 HOH HOH . J 6 HOH B 10 510 10 HOH HOH . J 6 HOH B 11 511 24 HOH HOH . J 6 HOH B 12 512 112 HOH HOH . J 6 HOH B 13 513 53 HOH HOH . J 6 HOH B 14 514 122 HOH HOH . J 6 HOH B 15 515 61 HOH HOH . J 6 HOH B 16 516 142 HOH HOH . J 6 HOH B 17 517 140 HOH HOH . J 6 HOH B 18 518 62 HOH HOH . J 6 HOH B 19 519 68 HOH HOH . J 6 HOH B 20 520 125 HOH HOH . J 6 HOH B 21 521 21 HOH HOH . J 6 HOH B 22 522 95 HOH HOH . J 6 HOH B 23 523 25 HOH HOH . J 6 HOH B 24 524 94 HOH HOH . J 6 HOH B 25 525 143 HOH HOH . J 6 HOH B 26 526 15 HOH HOH . J 6 HOH B 27 527 165 HOH HOH . J 6 HOH B 28 528 154 HOH HOH . J 6 HOH B 29 529 181 HOH HOH . J 6 HOH B 30 530 18 HOH HOH . J 6 HOH B 31 531 137 HOH HOH . J 6 HOH B 32 532 73 HOH HOH . J 6 HOH B 33 533 30 HOH HOH . J 6 HOH B 34 534 50 HOH HOH . J 6 HOH B 35 535 6 HOH HOH . J 6 HOH B 36 536 201 HOH HOH . J 6 HOH B 37 537 85 HOH HOH . J 6 HOH B 38 538 31 HOH HOH . J 6 HOH B 39 539 119 HOH HOH . J 6 HOH B 40 540 169 HOH HOH . J 6 HOH B 41 541 64 HOH HOH . J 6 HOH B 42 542 20 HOH HOH . J 6 HOH B 43 543 159 HOH HOH . J 6 HOH B 44 544 179 HOH HOH . J 6 HOH B 45 545 39 HOH HOH . J 6 HOH B 46 546 47 HOH HOH . J 6 HOH B 47 547 121 HOH HOH . J 6 HOH B 48 548 63 HOH HOH . J 6 HOH B 49 549 78 HOH HOH . J 6 HOH B 50 550 108 HOH HOH . J 6 HOH B 51 551 59 HOH HOH . J 6 HOH B 52 552 16 HOH HOH . J 6 HOH B 53 553 190 HOH HOH . J 6 HOH B 54 554 203 HOH HOH . J 6 HOH B 55 555 34 HOH HOH . J 6 HOH B 56 556 101 HOH HOH . J 6 HOH B 57 557 168 HOH HOH . J 6 HOH B 58 558 84 HOH HOH . J 6 HOH B 59 559 60 HOH HOH . J 6 HOH B 60 560 158 HOH HOH . J 6 HOH B 61 561 113 HOH HOH . J 6 HOH B 62 562 126 HOH HOH . J 6 HOH B 63 563 173 HOH HOH . J 6 HOH B 64 564 185 HOH HOH . J 6 HOH B 65 565 172 HOH HOH . J 6 HOH B 66 566 97 HOH HOH . J 6 HOH B 67 567 200 HOH HOH . J 6 HOH B 68 568 88 HOH HOH . J 6 HOH B 69 569 19 HOH HOH . J 6 HOH B 70 570 207 HOH HOH . J 6 HOH B 71 571 56 HOH HOH . J 6 HOH B 72 572 216 HOH HOH . J 6 HOH B 73 573 136 HOH HOH . J 6 HOH B 74 574 109 HOH HOH . J 6 HOH B 75 575 144 HOH HOH . J 6 HOH B 76 576 156 HOH HOH . J 6 HOH B 77 577 141 HOH HOH . J 6 HOH B 78 578 180 HOH HOH . J 6 HOH B 79 579 110 HOH HOH . J 6 HOH B 80 580 162 HOH HOH . J 6 HOH B 81 581 184 HOH HOH . J 6 HOH B 82 582 217 HOH HOH . J 6 HOH B 83 583 138 HOH HOH . J 6 HOH B 84 584 74 HOH HOH . J 6 HOH B 85 585 189 HOH HOH . J 6 HOH B 86 586 134 HOH HOH . J 6 HOH B 87 587 193 HOH HOH . J 6 HOH B 88 588 191 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 P TYM . . . G 5 -4.865 3.721 22.265 1 56.37 ? P TYM 402 B 1 HETATM 2 O O1P TYM . . . G 5 -4.114 4.9 22.749 1 51.57 ? O1P TYM 402 B 1 HETATM 3 O O2P TYM . . . G 5 -4.69 2.442 22.99 1 51.27 -1 O2P TYM 402 B 1 HETATM 4 O O5' TYM . . . G 5 -6.43 4.093 22.271 1 53.39 ? O5' TYM 402 B 1 HETATM 5 C C5' TYM . . . G 5 -7.431 3.041 22.309 1 52.8 ? C5' TYM 402 B 1 HETATM 6 C C4' TYM . . . G 5 -8.73 3.501 21.685 1 52.77 ? C4' TYM 402 B 1 HETATM 7 O O4' TYM . . . G 5 -9.474 4.32 22.614 1 50.82 ? O4' TYM 402 B 1 HETATM 8 C C1' TYM . . . G 5 -9.759 5.583 22.04 1 53.14 ? C1' TYM 402 B 1 HETATM 9 N N9 TYM . . . G 5 -9.702 6.597 23.093 1 57.32 ? N9 TYM 402 B 1 HETATM 10 C C4 TYM . . . G 5 -10.752 7.31 23.618 1 56.59 ? C4 TYM 402 B 1 HETATM 11 N N3 TYM . . . G 5 -12.037 7.276 23.234 1 58.97 ? N3 TYM 402 B 1 HETATM 12 C C2 TYM . . . G 5 -12.785 8.094 23.981 1 56.82 ? C2 TYM 402 B 1 HETATM 13 N N1 TYM . . . G 5 -12.409 8.888 24.991 1 56.36 ? N1 TYM 402 B 1 HETATM 14 C C6 TYM . . . G 5 -11.105 8.906 25.357 1 58.29 ? C6 TYM 402 B 1 HETATM 15 N N6 TYM . . . G 5 -10.748 9.662 26.41 1 57.01 ? N6 TYM 402 B 1 HETATM 16 C C5 TYM . . . G 5 -10.212 8.082 24.639 1 58.4 ? C5 TYM 402 B 1 HETATM 17 N N7 TYM . . . G 5 -8.846 7.863 24.748 1 55.15 ? N7 TYM 402 B 1 HETATM 18 C C8 TYM . . . G 5 -8.598 6.978 23.813 1 59.31 ? C8 TYM 402 B 1 HETATM 19 C C2' TYM . . . G 5 -8.746 5.772 20.918 1 53.11 ? C2' TYM 402 B 1 HETATM 20 O O2' TYM . . . G 5 -9.292 6.611 19.91 1 56.05 ? O2' TYM 402 B 1 HETATM 21 C C3' TYM . . . G 5 -8.586 4.331 20.41 1 53.19 ? C3' TYM 402 B 1 HETATM 22 O O3' TYM . . . G 5 -9.548 3.944 19.433 1 51.8 ? O3' TYM 402 B 1 HETATM 23 N NH3 TYM . . . G 5 -3.128 4.503 17.608 1 48.87 ? NH3 TYM 402 B 1 HETATM 24 C CA TYM . . . G 5 -4.216 3.769 18.317 1 47.24 ? CA TYM 402 B 1 HETATM 25 C CB TYM . . . G 5 -3.966 2.261 18.286 1 45.35 ? CB TYM 402 B 1 HETATM 26 C CG TYM . . . G 5 -3.796 1.707 16.903 1 40.55 ? CG TYM 402 B 1 HETATM 27 C CD2 TYM . . . G 5 -4.836 1.431 15.953 1 38.72 ? CD2 TYM 402 B 1 HETATM 28 C CE2 TYM . . . G 5 -4.219 0.9 14.806 1 40.64 ? CE2 TYM 402 B 1 HETATM 29 C CE3 TYM . . . G 5 -6.212 1.624 15.936 1 37.56 ? CE3 TYM 402 B 1 HETATM 30 C CD1 TYM . . . G 5 -2.627 1.345 16.304 1 40.91 ? CD1 TYM 402 B 1 HETATM 31 N NE1 TYM . . . G 5 -2.87 0.857 15.047 1 42.78 ? NE1 TYM 402 B 1 HETATM 32 C CZ2 TYM . . . G 5 -4.946 0.569 13.669 1 37.7 ? CZ2 TYM 402 B 1 HETATM 33 C CZ3 TYM . . . G 5 -6.944 1.294 14.802 1 40.58 ? CZ3 TYM 402 B 1 HETATM 34 C CH2 TYM . . . G 5 -6.317 0.772 13.681 1 39.34 ? CH2 TYM 402 B 1 HETATM 35 C C TYM . . . G 5 -4.333 4.32 19.727 1 48.61 ? C TYM 402 B 1 HETATM 36 O O TYM . . . G 5 -4.314 5.488 19.989 1 53.32 ? O TYM 402 B 1 HETATM 37 O OPP TYM . . . G 5 -4.475 3.389 20.709 1 54.46 ? OPP TYM 402 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 37 #