data_8I2A # _model_server_result.job_id waKIJ5fOuuViqTE5jSjaXg _model_server_result.datetime_utc '2024-11-12 20:53:14' _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 8i2a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8I2A # _exptl.entry_id 8I2A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 533.431 _entity.id 3 _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 106.3 _cell.angle_gamma 90 _cell.entry_id 8I2A _cell.length_a 61.741 _cell.length_b 80.539 _cell.length_c 77.258 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8I2A _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 _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 3 _struct_asym.id D _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 367 n n P O2P TYM doub 368 n n P O5' TYM sing 369 n n P OPP TYM sing 370 n n O1P H1PO TYM sing 371 n n O5' C5' TYM sing 372 n n C5' C4' TYM sing 373 n n C5' "H5'1" TYM sing 374 n n C5' "H5'2" TYM sing 375 n n C4' O4' TYM sing 376 n n C4' C3' TYM sing 377 n n C4' "H4'C" TYM sing 378 n n O4' C1' TYM sing 379 n n C1' N9 TYM sing 380 n n C1' C2' TYM sing 381 n n C1' "H1'C" TYM sing 382 n n N9 C4 TYM sing 383 n y N9 C8 TYM sing 384 n y C4 N3 TYM doub 385 n y C4 C5 TYM sing 386 n y N3 C2 TYM sing 387 n y C2 N1 TYM doub 388 n y C2 HC2 TYM sing 389 n n N1 C6 TYM sing 390 n y C6 N6 TYM sing 391 n n C6 C5 TYM doub 392 n y N6 HN61 TYM sing 393 n n N6 HN62 TYM sing 394 n n C5 N7 TYM sing 395 n y N7 C8 TYM doub 396 n y C8 HC8 TYM sing 397 n n C2' O2' TYM sing 398 n n C2' C3' TYM sing 399 n n C2' "H2'C" TYM sing 400 n n O2' "H2'O" TYM sing 401 n n C3' O3' TYM sing 402 n n C3' "H3'C" TYM sing 403 n n O3' "H3'O" TYM sing 404 n n NH3 CA TYM sing 405 n n NH3 HH31 TYM sing 406 n n NH3 HH32 TYM sing 407 n n CA CB TYM sing 408 n n CA C TYM sing 409 n n CA HCA TYM sing 410 n n CB CG TYM sing 411 n n CB HCB1 TYM sing 412 n n CB HCB2 TYM sing 413 n n CG CD2 TYM sing 414 n y CG CD1 TYM doub 415 n y CD2 CE2 TYM doub 416 n y CD2 CE3 TYM sing 417 n y CE2 NE1 TYM sing 418 n y CE2 CZ2 TYM sing 419 n y CE3 CZ3 TYM doub 420 n y CE3 HE3C TYM sing 421 n n CD1 NE1 TYM sing 422 n y CD1 HD1C TYM sing 423 n n NE1 HE1N TYM sing 424 n n CZ2 CH2 TYM doub 425 n y CZ2 HZ2C TYM sing 426 n n CZ3 CH2 TYM sing 427 n y CZ3 HZ3C TYM sing 428 n n CH2 HH2C TYM sing 429 n n C O TYM doub 430 n n C OPP TYM sing 431 n n # _atom_sites.entry_id 8I2A _atom_sites.fract_transf_matrix[1][1] 0.016197 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004737 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012416 _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] 0.013486 _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 SO4 A 1 401 2 SO4 SO4 . D 3 TYM B 1 401 401 TYM TYM . E 4 EDO B 1 402 1 EDO EDO . F 2 SO4 B 1 403 1 SO4 SO4 . G 5 5OB B 1 404 1 5OB 5OB . H 6 HOH A 1 501 64 HOH HOH . H 6 HOH A 2 502 78 HOH HOH . H 6 HOH A 3 503 80 HOH HOH . H 6 HOH A 4 504 61 HOH HOH . H 6 HOH A 5 505 77 HOH HOH . H 6 HOH A 6 506 35 HOH HOH . H 6 HOH A 7 507 11 HOH HOH . H 6 HOH A 8 508 70 HOH HOH . H 6 HOH A 9 509 18 HOH HOH . H 6 HOH A 10 510 52 HOH HOH . H 6 HOH A 11 511 49 HOH HOH . H 6 HOH A 12 512 26 HOH HOH . H 6 HOH A 13 513 73 HOH HOH . H 6 HOH A 14 514 21 HOH HOH . H 6 HOH A 15 515 23 HOH HOH . H 6 HOH A 16 516 34 HOH HOH . H 6 HOH A 17 517 112 HOH HOH . H 6 HOH A 18 518 39 HOH HOH . H 6 HOH A 19 519 109 HOH HOH . H 6 HOH A 20 520 13 HOH HOH . H 6 HOH A 21 521 12 HOH HOH . H 6 HOH A 22 522 104 HOH HOH . H 6 HOH A 23 523 50 HOH HOH . H 6 HOH A 24 524 115 HOH HOH . H 6 HOH A 25 525 47 HOH HOH . H 6 HOH A 26 526 6 HOH HOH . H 6 HOH A 27 527 63 HOH HOH . H 6 HOH A 28 528 76 HOH HOH . H 6 HOH A 29 529 71 HOH HOH . H 6 HOH A 30 530 46 HOH HOH . H 6 HOH A 31 531 113 HOH HOH . H 6 HOH A 32 532 40 HOH HOH . H 6 HOH A 33 533 87 HOH HOH . H 6 HOH A 34 534 62 HOH HOH . H 6 HOH A 35 535 32 HOH HOH . H 6 HOH A 36 536 1 HOH HOH . H 6 HOH A 37 537 60 HOH HOH . H 6 HOH A 38 538 107 HOH HOH . H 6 HOH A 39 539 105 HOH HOH . H 6 HOH A 40 540 53 HOH HOH . H 6 HOH A 41 541 110 HOH HOH . H 6 HOH A 42 542 103 HOH HOH . H 6 HOH A 43 543 106 HOH HOH . H 6 HOH A 44 544 85 HOH HOH . H 6 HOH A 45 545 114 HOH HOH . H 6 HOH A 46 546 51 HOH HOH . H 6 HOH A 47 547 108 HOH HOH . H 6 HOH A 48 548 79 HOH HOH . H 6 HOH A 49 549 119 HOH HOH . H 6 HOH A 50 550 101 HOH HOH . H 6 HOH A 51 551 86 HOH HOH . H 6 HOH A 52 552 100 HOH HOH . H 6 HOH A 53 553 102 HOH HOH . H 6 HOH A 54 554 84 HOH HOH . H 6 HOH A 55 555 88 HOH HOH . I 6 HOH B 1 501 75 HOH HOH . I 6 HOH B 2 502 55 HOH HOH . I 6 HOH B 3 503 30 HOH HOH . I 6 HOH B 4 504 5 HOH HOH . I 6 HOH B 5 505 91 HOH HOH . I 6 HOH B 6 506 7 HOH HOH . I 6 HOH B 7 507 67 HOH HOH . I 6 HOH B 8 508 4 HOH HOH . I 6 HOH B 9 509 2 HOH HOH . I 6 HOH B 10 510 59 HOH HOH . I 6 HOH B 11 511 9 HOH HOH . I 6 HOH B 12 512 15 HOH HOH . I 6 HOH B 13 513 27 HOH HOH . I 6 HOH B 14 514 17 HOH HOH . I 6 HOH B 15 515 68 HOH HOH . I 6 HOH B 16 516 83 HOH HOH . I 6 HOH B 17 517 10 HOH HOH . I 6 HOH B 18 518 14 HOH HOH . I 6 HOH B 19 519 43 HOH HOH . I 6 HOH B 20 520 42 HOH HOH . I 6 HOH B 21 521 31 HOH HOH . I 6 HOH B 22 522 22 HOH HOH . I 6 HOH B 23 523 25 HOH HOH . I 6 HOH B 24 524 29 HOH HOH . I 6 HOH B 25 525 98 HOH HOH . I 6 HOH B 26 526 116 HOH HOH . I 6 HOH B 27 527 57 HOH HOH . I 6 HOH B 28 528 38 HOH HOH . I 6 HOH B 29 529 41 HOH HOH . I 6 HOH B 30 530 16 HOH HOH . I 6 HOH B 31 531 8 HOH HOH . I 6 HOH B 32 532 37 HOH HOH . I 6 HOH B 33 533 44 HOH HOH . I 6 HOH B 34 534 24 HOH HOH . I 6 HOH B 35 535 45 HOH HOH . I 6 HOH B 36 536 54 HOH HOH . I 6 HOH B 37 537 118 HOH HOH . I 6 HOH B 38 538 94 HOH HOH . I 6 HOH B 39 539 33 HOH HOH . I 6 HOH B 40 540 82 HOH HOH . I 6 HOH B 41 541 69 HOH HOH . I 6 HOH B 42 542 97 HOH HOH . I 6 HOH B 43 543 3 HOH HOH . I 6 HOH B 44 544 20 HOH HOH . I 6 HOH B 45 545 56 HOH HOH . I 6 HOH B 46 546 58 HOH HOH . I 6 HOH B 47 547 72 HOH HOH . I 6 HOH B 48 548 36 HOH HOH . I 6 HOH B 49 549 19 HOH HOH . I 6 HOH B 50 550 89 HOH HOH . I 6 HOH B 51 551 93 HOH HOH . I 6 HOH B 52 552 92 HOH HOH . I 6 HOH B 53 553 48 HOH HOH . I 6 HOH B 54 554 117 HOH HOH . I 6 HOH B 55 555 81 HOH HOH . I 6 HOH B 56 556 66 HOH HOH . I 6 HOH B 57 557 74 HOH HOH . I 6 HOH B 58 558 95 HOH HOH . I 6 HOH B 59 559 96 HOH HOH . I 6 HOH B 60 560 90 HOH HOH . I 6 HOH B 61 561 28 HOH HOH . I 6 HOH B 62 562 99 HOH HOH . I 6 HOH B 63 563 65 HOH HOH . I 6 HOH B 64 564 111 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 . . . D 3 -4.879 3.767 21.732 1 41.33 ? P TYM 401 B 1 HETATM 2 O O1P TYM . . . D 3 -4.803 2.509 22.563 1 41.26 ? O1P TYM 401 B 1 HETATM 3 O O2P TYM . . . D 3 -4.253 5.045 22.238 1 41.64 ? O2P TYM 401 B 1 HETATM 4 O O5' TYM . . . D 3 -6.431 4.061 21.421 1 41.71 ? O5' TYM 401 B 1 HETATM 5 C C5' TYM . . . D 3 -7.368 2.986 21.336 1 42.09 ? C5' TYM 401 B 1 HETATM 6 C C4' TYM . . . D 3 -8.706 3.463 20.78 1 42.24 ? C4' TYM 401 B 1 HETATM 7 O O4' TYM . . . D 3 -9.397 4.23 21.77 1 42.21 ? O4' TYM 401 B 1 HETATM 8 C C1' TYM . . . D 3 -9.746 5.52 21.254 1 42.43 ? C1' TYM 401 B 1 HETATM 9 N N9 TYM . . . D 3 -9.625 6.534 22.332 1 42.32 ? N9 TYM 401 B 1 HETATM 10 C C4 TYM . . . D 3 -10.639 7.241 22.823 1 42.04 ? C4 TYM 401 B 1 HETATM 11 N N3 TYM . . . D 3 -11.964 7.315 22.548 1 41.86 ? N3 TYM 401 B 1 HETATM 12 C C2 TYM . . . D 3 -12.774 8.154 23.224 1 41.92 ? C2 TYM 401 B 1 HETATM 13 N N1 TYM . . . D 3 -12.33 8.969 24.208 1 42.05 ? N1 TYM 401 B 1 HETATM 14 C C6 TYM . . . D 3 -11.027 9.002 24.585 1 42.16 ? C6 TYM 401 B 1 HETATM 15 N N6 TYM . . . D 3 -10.604 9.829 25.57 1 42.05 ? N6 TYM 401 B 1 HETATM 16 C C5 TYM . . . D 3 -10.078 8.1 23.879 1 42.13 ? C5 TYM 401 B 1 HETATM 17 N N7 TYM . . . D 3 -8.762 7.824 23.932 1 42.42 ? N7 TYM 401 B 1 HETATM 18 C C8 TYM . . . D 3 -8.506 6.873 22.995 1 42.59 ? C8 TYM 401 B 1 HETATM 19 C C2' TYM . . . D 3 -8.834 5.759 20.061 1 42.42 ? C2' TYM 401 B 1 HETATM 20 O O2' TYM . . . D 3 -9.474 6.579 19.082 1 42.48 ? O2' TYM 401 B 1 HETATM 21 C C3' TYM . . . D 3 -8.564 4.356 19.551 1 42.47 ? C3' TYM 401 B 1 HETATM 22 O O3' TYM . . . D 3 -9.52 3.965 18.561 1 42.48 ? O3' TYM 401 B 1 HETATM 23 N NH3 TYM . . . D 3 -3.418 4.522 16.904 1 39.2 ? NH3 TYM 401 B 1 HETATM 24 C CA TYM . . . D 3 -4.351 3.773 17.728 1 39.4 ? CA TYM 401 B 1 HETATM 25 C CB TYM . . . D 3 -3.968 2.297 17.731 1 38.42 ? CB TYM 401 B 1 HETATM 26 C CG TYM . . . D 3 -3.891 1.712 16.34 1 37.83 ? CG TYM 401 B 1 HETATM 27 C CD2 TYM . . . D 3 -4.985 1.49 15.372 1 37.4 ? CD2 TYM 401 B 1 HETATM 28 C CE2 TYM . . . D 3 -4.346 0.881 14.192 1 37.29 ? CE2 TYM 401 B 1 HETATM 29 C CE3 TYM . . . D 3 -6.352 1.739 15.396 1 37.29 ? CE3 TYM 401 B 1 HETATM 30 C CD1 TYM . . . D 3 -2.746 1.245 15.704 1 37.6 ? CD1 TYM 401 B 1 HETATM 31 N NE1 TYM . . . D 3 -3.032 0.769 14.458 1 37.47 ? NE1 TYM 401 B 1 HETATM 32 C CZ2 TYM . . . D 3 -5.148 0.562 13.098 1 37.1 ? CZ2 TYM 401 B 1 HETATM 33 C CZ3 TYM . . . D 3 -7.115 1.397 14.274 1 37.12 ? CZ3 TYM 401 B 1 HETATM 34 C CH2 TYM . . . D 3 -6.522 0.819 13.143 1 36.94 ? CH2 TYM 401 B 1 HETATM 35 C C TYM . . . D 3 -4.34 4.313 19.136 1 40.55 ? C TYM 401 B 1 HETATM 36 O O TYM . . . D 3 -4.397 5.516 19.328 1 42.13 ? O TYM 401 B 1 HETATM 37 O OPP TYM . . . D 3 -4.254 3.417 20.286 1 41.57 ? OPP TYM 401 B 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 37 #