data_8I2J # _model_server_result.job_id syZQ232duumuZrCQNu_yvg _model_server_result.datetime_utc '2024-11-18 14:53:28' _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 8i2j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8I2J # _exptl.entry_id 8I2J _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 105.65 _cell.angle_gamma 90 _cell.entry_id 8I2J _cell.length_a 61.795 _cell.length_b 80.423 _cell.length_c 78.658 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8I2J _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 _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 359 n n P O2P TYM doub 360 n n P O5' TYM sing 361 n n P OPP TYM sing 362 n n O1P H1PO TYM sing 363 n n O5' C5' TYM sing 364 n n C5' C4' TYM sing 365 n n C5' "H5'1" TYM sing 366 n n C5' "H5'2" TYM sing 367 n n C4' O4' TYM sing 368 n n C4' C3' TYM sing 369 n n C4' "H4'C" TYM sing 370 n n O4' C1' TYM sing 371 n n C1' N9 TYM sing 372 n n C1' C2' TYM sing 373 n n C1' "H1'C" TYM sing 374 n n N9 C4 TYM sing 375 n y N9 C8 TYM sing 376 n y C4 N3 TYM doub 377 n y C4 C5 TYM sing 378 n y N3 C2 TYM sing 379 n y C2 N1 TYM doub 380 n y C2 HC2 TYM sing 381 n n N1 C6 TYM sing 382 n y C6 N6 TYM sing 383 n n C6 C5 TYM doub 384 n y N6 HN61 TYM sing 385 n n N6 HN62 TYM sing 386 n n C5 N7 TYM sing 387 n y N7 C8 TYM doub 388 n y C8 HC8 TYM sing 389 n n C2' O2' TYM sing 390 n n C2' C3' TYM sing 391 n n C2' "H2'C" TYM sing 392 n n O2' "H2'O" TYM sing 393 n n C3' O3' TYM sing 394 n n C3' "H3'C" TYM sing 395 n n O3' "H3'O" TYM sing 396 n n NH3 CA TYM sing 397 n n NH3 HH31 TYM sing 398 n n NH3 HH32 TYM sing 399 n n CA CB TYM sing 400 n n CA C TYM sing 401 n n CA HCA TYM sing 402 n n CB CG TYM sing 403 n n CB HCB1 TYM sing 404 n n CB HCB2 TYM sing 405 n n CG CD2 TYM sing 406 n y CG CD1 TYM doub 407 n y CD2 CE2 TYM doub 408 n y CD2 CE3 TYM sing 409 n y CE2 NE1 TYM sing 410 n y CE2 CZ2 TYM sing 411 n y CE3 CZ3 TYM doub 412 n y CE3 HE3C TYM sing 413 n n CD1 NE1 TYM sing 414 n y CD1 HD1C TYM sing 415 n n NE1 HE1N TYM sing 416 n n CZ2 CH2 TYM doub 417 n y CZ2 HZ2C TYM sing 418 n n CZ3 CH2 TYM sing 419 n y CZ3 HZ3C TYM sing 420 n n CH2 HH2C TYM sing 421 n n C O TYM doub 422 n n C OPP TYM sing 423 n n # _atom_sites.entry_id 8I2J _atom_sites.fract_transf_matrix[1][1] 0.016183 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004533 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012434 _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] 0.013203 _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 O9F A 1 401 1 O9F 140 . D 3 TYM B 1 401 401 TYM TYM . E 4 SO4 B 1 402 1 SO4 SO4 . F 5 HOH A 1 501 41 HOH HOH . F 5 HOH A 2 502 43 HOH HOH . F 5 HOH A 3 503 50 HOH HOH . F 5 HOH A 4 504 8 HOH HOH . F 5 HOH A 5 505 20 HOH HOH . F 5 HOH A 6 506 12 HOH HOH . F 5 HOH A 7 507 5 HOH HOH . F 5 HOH A 8 508 66 HOH HOH . F 5 HOH A 9 509 4 HOH HOH . F 5 HOH A 10 510 37 HOH HOH . F 5 HOH A 11 511 60 HOH HOH . F 5 HOH A 12 512 49 HOH HOH . F 5 HOH A 13 513 61 HOH HOH . F 5 HOH A 14 514 51 HOH HOH . F 5 HOH A 15 515 3 HOH HOH . F 5 HOH A 16 516 46 HOH HOH . F 5 HOH A 17 517 9 HOH HOH . F 5 HOH A 18 518 64 HOH HOH . F 5 HOH A 19 519 34 HOH HOH . F 5 HOH A 20 520 67 HOH HOH . F 5 HOH A 21 521 32 HOH HOH . F 5 HOH A 22 522 71 HOH HOH . F 5 HOH A 23 523 63 HOH HOH . F 5 HOH A 24 524 38 HOH HOH . F 5 HOH A 25 525 23 HOH HOH . F 5 HOH A 26 526 10 HOH HOH . F 5 HOH A 27 527 57 HOH HOH . F 5 HOH A 28 528 54 HOH HOH . F 5 HOH A 29 529 59 HOH HOH . F 5 HOH A 30 530 65 HOH HOH . F 5 HOH A 31 531 58 HOH HOH . F 5 HOH A 32 532 42 HOH HOH . G 5 HOH B 1 501 27 HOH HOH . G 5 HOH B 2 502 7 HOH HOH . G 5 HOH B 3 503 55 HOH HOH . G 5 HOH B 4 504 17 HOH HOH . G 5 HOH B 5 505 22 HOH HOH . G 5 HOH B 6 506 62 HOH HOH . G 5 HOH B 7 507 44 HOH HOH . G 5 HOH B 8 508 72 HOH HOH . G 5 HOH B 9 509 6 HOH HOH . G 5 HOH B 10 510 1 HOH HOH . G 5 HOH B 11 511 40 HOH HOH . G 5 HOH B 12 512 53 HOH HOH . G 5 HOH B 13 513 16 HOH HOH . G 5 HOH B 14 514 52 HOH HOH . G 5 HOH B 15 515 36 HOH HOH . G 5 HOH B 16 516 70 HOH HOH . G 5 HOH B 17 517 47 HOH HOH . G 5 HOH B 18 518 31 HOH HOH . G 5 HOH B 19 519 39 HOH HOH . G 5 HOH B 20 520 18 HOH HOH . G 5 HOH B 21 521 48 HOH HOH . G 5 HOH B 22 522 68 HOH HOH . G 5 HOH B 23 523 13 HOH HOH . G 5 HOH B 24 524 14 HOH HOH . G 5 HOH B 25 525 56 HOH HOH . G 5 HOH B 26 526 28 HOH HOH . G 5 HOH B 27 527 26 HOH HOH . G 5 HOH B 28 528 15 HOH HOH . G 5 HOH B 29 529 45 HOH HOH . G 5 HOH B 30 530 30 HOH HOH . G 5 HOH B 31 531 21 HOH HOH . G 5 HOH B 32 532 25 HOH HOH . G 5 HOH B 33 533 35 HOH HOH . G 5 HOH B 34 534 24 HOH HOH . G 5 HOH B 35 535 33 HOH HOH . G 5 HOH B 36 536 29 HOH HOH . G 5 HOH B 37 537 11 HOH HOH . G 5 HOH B 38 538 2 HOH HOH . G 5 HOH B 39 539 19 HOH HOH . G 5 HOH B 40 540 69 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 -4.805 3.488 22.414 1 24.47 ? P TYM 401 B 1 HETATM 2 O O1P TYM . . . D 3 -4.717 2.195 23.191 1 24.5 ? O1P TYM 401 B 1 HETATM 3 O O2P TYM . . . D 3 -4.092 4.723 22.908 1 24.56 ? O2P TYM 401 B 1 HETATM 4 O O5' TYM . . . D 3 -6.362 3.838 22.221 1 24.93 ? O5' TYM 401 B 1 HETATM 5 C C5' TYM . . . D 3 -7.312 2.78 22.115 1 25.41 ? C5' TYM 401 B 1 HETATM 6 C C4' TYM . . . D 3 -8.63 3.289 21.547 1 25.8 ? C4' TYM 401 B 1 HETATM 7 O O4' TYM . . . D 3 -9.294 4.101 22.52 1 26.01 ? O4' TYM 401 B 1 HETATM 8 C C1' TYM . . . D 3 -9.609 5.388 21.981 1 26.14 ? C1' TYM 401 B 1 HETATM 9 N N9 TYM . . . D 3 -9.446 6.413 23.05 1 26.31 ? N9 TYM 401 B 1 HETATM 10 C C4 TYM . . . D 3 -10.453 7.113 23.571 1 26.25 ? C4 TYM 401 B 1 HETATM 11 N N3 TYM . . . D 3 -11.789 7.174 23.341 1 26.32 ? N3 TYM 401 B 1 HETATM 12 C C2 TYM . . . D 3 -12.59 8.011 24.034 1 26.36 ? C2 TYM 401 B 1 HETATM 13 N N1 TYM . . . D 3 -12.124 8.838 24.995 1 26.21 ? N1 TYM 401 B 1 HETATM 14 C C6 TYM . . . D 3 -10.811 8.884 25.329 1 26.28 ? C6 TYM 401 B 1 HETATM 15 N N6 TYM . . . D 3 -10.38 9.726 26.295 1 26.35 ? N6 TYM 401 B 1 HETATM 16 C C5 TYM . . . D 3 -9.87 7.986 24.603 1 26.32 ? C5 TYM 401 B 1 HETATM 17 N N7 TYM . . . D 3 -8.551 7.724 24.617 1 26.29 ? N7 TYM 401 B 1 HETATM 18 C C8 TYM . . . D 3 -8.307 6.769 23.68 1 26.45 ? C8 TYM 401 B 1 HETATM 19 C C2' TYM . . . D 3 -8.71 5.566 20.765 1 26.06 ? C2' TYM 401 B 1 HETATM 20 O O2' TYM . . . D 3 -9.345 6.356 19.759 1 25.99 ? O2' TYM 401 B 1 HETATM 21 C C3' TYM . . . D 3 -8.451 4.142 20.295 1 26.05 ? C3' TYM 401 B 1 HETATM 22 O O3' TYM . . . D 3 -9.369 3.705 19.283 1 25.87 ? O3' TYM 401 B 1 HETATM 23 N NH3 TYM . . . D 3 -3.483 4.387 17.626 1 22.49 ? NH3 TYM 401 B 1 HETATM 24 C CA TYM . . . D 3 -4.431 3.579 18.365 1 22.7 ? CA TYM 401 B 1 HETATM 25 C CB TYM . . . D 3 -3.992 2.119 18.346 1 22.28 ? CB TYM 401 B 1 HETATM 26 C CG TYM . . . D 3 -3.94 1.545 16.95 1 21.97 ? CG TYM 401 B 1 HETATM 27 C CD2 TYM . . . D 3 -5.036 1.345 15.978 1 21.85 ? CD2 TYM 401 B 1 HETATM 28 C CE2 TYM . . . D 3 -4.401 0.735 14.793 1 21.75 ? CE2 TYM 401 B 1 HETATM 29 C CE3 TYM . . . D 3 -6.4 1.615 15.993 1 21.84 ? CE3 TYM 401 B 1 HETATM 30 C CD1 TYM . . . D 3 -2.804 1.064 16.314 1 21.85 ? CD1 TYM 401 B 1 HETATM 31 N NE1 TYM . . . D 3 -3.093 0.602 15.065 1 21.84 ? NE1 TYM 401 B 1 HETATM 32 C CZ2 TYM . . . D 3 -5.198 0.435 13.691 1 21.58 ? CZ2 TYM 401 B 1 HETATM 33 C CZ3 TYM . . . D 3 -7.158 1.289 14.861 1 21.72 ? CZ3 TYM 401 B 1 HETATM 34 C CH2 TYM . . . D 3 -6.567 0.711 13.73 1 21.61 ? CH2 TYM 401 B 1 HETATM 35 C C TYM . . . D 3 -4.519 4.078 19.782 1 23.26 ? C TYM 401 B 1 HETATM 36 O O TYM . . . D 3 -4.775 5.249 19.996 1 23.51 ? O TYM 401 B 1 HETATM 37 O OPP TYM . . . D 3 -4.3 3.179 20.912 1 24.2 ? OPP TYM 401 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 37 #