data_3EP8 # _model_server_result.job_id N5b426AkiTMc4N0qncIO3g _model_server_result.datetime_utc '2024-11-27 00:13:31' _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 3ep8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":368}' # _entry.id 3EP8 # _exptl.entry_id 3EP8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 414.48 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'S-ADENOSYLMETHIONINE METHYL 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 105.39 _cell.angle_gamma 90 _cell.entry_id 3EP8 _cell.length_a 100.146 _cell.length_b 51.073 _cell.length_c 68.947 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EP8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 _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 4 _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 covale ? covale1 C C PYR . A PYR 68 1_555 B N SER 1 A SER 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale2 C CA PYR . A PYR 68 1_555 D N SMM . A SMM 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? # _chem_comp.formula 'C16 H26 N6 O5 S' _chem_comp.formula_weight 414.48 _chem_comp.id SMM _chem_comp.mon_nstd_flag . _chem_comp.name 'S-ADENOSYLMETHIONINE METHYL 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 N CA SMM sing 299 n n N HN1 SMM sing 300 n n N HN2 SMM sing 301 n n CA CB SMM sing 302 n n CA C SMM sing 303 n n CA HA1 SMM sing 304 n n CB CG SMM sing 305 n n CB HB1 SMM sing 306 n n CB HB2 SMM sing 307 n n CG SD SMM sing 308 n n CG HG1 SMM sing 309 n n CG HG2 SMM sing 310 n n SD CE SMM sing 311 n n SD C5' SMM sing 312 n n SD HD1 SMM sing 313 n n CE HE1 SMM sing 314 n n CE HE2 SMM sing 315 n n CE HE3 SMM sing 316 n n C5' C4' SMM sing 317 n n C5' "H5'1" SMM sing 318 n n C5' "H5'2" SMM sing 319 n n C4' O4' SMM sing 320 n n C4' C3' SMM sing 321 n n C4' H4' SMM sing 322 n n O4' C1' SMM sing 323 n n C1' N9 SMM sing 324 n n C1' C2' SMM sing 325 n n C1' H1' SMM sing 326 n n N9 C4 SMM sing 327 n y N9 C8 SMM sing 328 n y C4 N3 SMM doub 329 n y C4 C5 SMM sing 330 n y N3 C2 SMM sing 331 n y C2 N1 SMM doub 332 n y C2 H2 SMM sing 333 n n N1 C6 SMM sing 334 n y C6 N6 SMM sing 335 n n C6 C5 SMM doub 336 n y N6 HN61 SMM sing 337 n n N6 HN62 SMM sing 338 n n C5 N7 SMM sing 339 n y N7 C8 SMM doub 340 n y C8 H8 SMM sing 341 n n C2' O2' SMM sing 342 n n C2' C3' SMM sing 343 n n C2' H2' SMM sing 344 n n O2' HO2' SMM sing 345 n n C3' O3' SMM sing 346 n n C3' H3' SMM sing 347 n n O3' HO3' SMM sing 348 n n C O SMM doub 349 n n C OXT SMM sing 350 n n OXT CXT SMM sing 351 n n CXT HXT1 SMM sing 352 n n CXT HXT2 SMM sing 353 n n CXT HXT3 SMM sing 354 n n # _atom_sites.entry_id 3EP8 _atom_sites.fract_transf_matrix[1][1] 0.009985 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002749 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01958 _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] 0.015044 _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 3 PYR A 1 68 68 PYR PYR . D 4 SMM A 1 368 368 SMM SMM . E 5 HOH B 1 330 330 HOH HOH . E 5 HOH B 2 338 338 HOH HOH . E 5 HOH B 3 340 340 HOH HOH . E 5 HOH B 4 341 341 HOH HOH . E 5 HOH B 5 347 347 HOH HOH . E 5 HOH B 6 355 355 HOH HOH . E 5 HOH B 7 356 356 HOH HOH . E 5 HOH B 8 366 366 HOH HOH . E 5 HOH B 9 367 367 HOH HOH . E 5 HOH B 10 369 369 HOH HOH . E 5 HOH B 11 370 370 HOH HOH . E 5 HOH B 12 375 375 HOH HOH . E 5 HOH B 13 386 386 HOH HOH . E 5 HOH B 14 389 389 HOH HOH . E 5 HOH B 15 390 390 HOH HOH . E 5 HOH B 16 392 392 HOH HOH . E 5 HOH B 17 394 394 HOH HOH . E 5 HOH B 18 395 395 HOH HOH . E 5 HOH B 19 405 405 HOH HOH . E 5 HOH B 20 406 406 HOH HOH . E 5 HOH B 21 407 407 HOH HOH . E 5 HOH B 22 410 410 HOH HOH . E 5 HOH B 23 430 430 HOH HOH . E 5 HOH B 24 433 433 HOH HOH . E 5 HOH B 25 441 441 HOH HOH . E 5 HOH B 26 442 442 HOH HOH . E 5 HOH B 27 450 450 HOH HOH . E 5 HOH B 28 455 455 HOH HOH . E 5 HOH B 29 462 462 HOH HOH . E 5 HOH B 30 475 475 HOH HOH . E 5 HOH B 31 486 486 HOH HOH . E 5 HOH B 32 492 492 HOH HOH . E 5 HOH B 33 493 493 HOH HOH . E 5 HOH B 34 496 496 HOH HOH . E 5 HOH B 35 512 512 HOH HOH . E 5 HOH B 36 525 525 HOH HOH . E 5 HOH B 37 533 533 HOH HOH . E 5 HOH B 38 541 541 HOH HOH . E 5 HOH B 39 542 542 HOH HOH . E 5 HOH B 40 543 543 HOH HOH . E 5 HOH B 41 544 544 HOH HOH . E 5 HOH B 42 545 545 HOH HOH . E 5 HOH B 43 546 546 HOH HOH . F 5 HOH A 1 331 331 HOH HOH . F 5 HOH A 2 332 332 HOH HOH . F 5 HOH A 3 333 333 HOH HOH . F 5 HOH A 4 334 334 HOH HOH . F 5 HOH A 5 335 335 HOH HOH . F 5 HOH A 6 336 336 HOH HOH . F 5 HOH A 7 337 337 HOH HOH . F 5 HOH A 8 339 339 HOH HOH . F 5 HOH A 9 342 342 HOH HOH . F 5 HOH A 10 343 343 HOH HOH . F 5 HOH A 11 344 344 HOH HOH . F 5 HOH A 12 345 345 HOH HOH . F 5 HOH A 13 348 348 HOH HOH . F 5 HOH A 14 349 349 HOH HOH . F 5 HOH A 15 350 350 HOH HOH . F 5 HOH A 16 351 351 HOH HOH . F 5 HOH A 17 352 352 HOH HOH . F 5 HOH A 18 353 353 HOH HOH . F 5 HOH A 19 354 354 HOH HOH . F 5 HOH A 20 357 357 HOH HOH . F 5 HOH A 21 358 358 HOH HOH . F 5 HOH A 22 359 359 HOH HOH . F 5 HOH A 23 360 360 HOH HOH . F 5 HOH A 24 361 361 HOH HOH . F 5 HOH A 25 362 362 HOH HOH . F 5 HOH A 26 363 363 HOH HOH . F 5 HOH A 27 365 365 HOH HOH . F 5 HOH A 28 371 371 HOH HOH . F 5 HOH A 29 373 373 HOH HOH . F 5 HOH A 30 374 374 HOH HOH . F 5 HOH A 31 376 376 HOH HOH . F 5 HOH A 32 377 377 HOH HOH . F 5 HOH A 33 379 379 HOH HOH . F 5 HOH A 34 380 380 HOH HOH . F 5 HOH A 35 381 381 HOH HOH . F 5 HOH A 36 382 382 HOH HOH . F 5 HOH A 37 384 384 HOH HOH . F 5 HOH A 38 385 385 HOH HOH . F 5 HOH A 39 387 387 HOH HOH . F 5 HOH A 40 388 388 HOH HOH . F 5 HOH A 41 393 393 HOH HOH . F 5 HOH A 42 396 396 HOH HOH . F 5 HOH A 43 397 397 HOH HOH . F 5 HOH A 44 398 398 HOH HOH . F 5 HOH A 45 399 399 HOH HOH . F 5 HOH A 46 400 400 HOH HOH . F 5 HOH A 47 401 401 HOH HOH . F 5 HOH A 48 402 402 HOH HOH . F 5 HOH A 49 403 403 HOH HOH . F 5 HOH A 50 404 404 HOH HOH . F 5 HOH A 51 408 408 HOH HOH . F 5 HOH A 52 409 409 HOH HOH . F 5 HOH A 53 411 411 HOH HOH . F 5 HOH A 54 412 412 HOH HOH . F 5 HOH A 55 413 413 HOH HOH . F 5 HOH A 56 414 414 HOH HOH . F 5 HOH A 57 415 415 HOH HOH . F 5 HOH A 58 416 416 HOH HOH . F 5 HOH A 59 417 417 HOH HOH . F 5 HOH A 60 418 418 HOH HOH . F 5 HOH A 61 419 419 HOH HOH . F 5 HOH A 62 420 420 HOH HOH . F 5 HOH A 63 421 421 HOH HOH . F 5 HOH A 64 422 422 HOH HOH . F 5 HOH A 65 423 423 HOH HOH . F 5 HOH A 66 424 424 HOH HOH . F 5 HOH A 67 425 425 HOH HOH . F 5 HOH A 68 426 426 HOH HOH . F 5 HOH A 69 427 427 HOH HOH . F 5 HOH A 70 428 428 HOH HOH . F 5 HOH A 71 429 429 HOH HOH . F 5 HOH A 72 431 431 HOH HOH . F 5 HOH A 73 432 432 HOH HOH . F 5 HOH A 74 434 434 HOH HOH . F 5 HOH A 75 435 435 HOH HOH . F 5 HOH A 76 436 436 HOH HOH . F 5 HOH A 77 437 437 HOH HOH . F 5 HOH A 78 438 438 HOH HOH . F 5 HOH A 79 439 439 HOH HOH . F 5 HOH A 80 440 440 HOH HOH . F 5 HOH A 81 443 443 HOH HOH . F 5 HOH A 82 444 444 HOH HOH . F 5 HOH A 83 445 445 HOH HOH . F 5 HOH A 84 446 446 HOH HOH . F 5 HOH A 85 447 447 HOH HOH . F 5 HOH A 86 448 448 HOH HOH . F 5 HOH A 87 449 449 HOH HOH . F 5 HOH A 88 451 451 HOH HOH . F 5 HOH A 89 452 452 HOH HOH . F 5 HOH A 90 453 453 HOH HOH . F 5 HOH A 91 454 454 HOH HOH . F 5 HOH A 92 456 456 HOH HOH . F 5 HOH A 93 457 457 HOH HOH . F 5 HOH A 94 458 458 HOH HOH . F 5 HOH A 95 459 459 HOH HOH . F 5 HOH A 96 460 460 HOH HOH . F 5 HOH A 97 461 461 HOH HOH . F 5 HOH A 98 463 463 HOH HOH . F 5 HOH A 99 464 464 HOH HOH . F 5 HOH A 100 465 465 HOH HOH . F 5 HOH A 101 466 466 HOH HOH . F 5 HOH A 102 467 467 HOH HOH . F 5 HOH A 103 468 468 HOH HOH . F 5 HOH A 104 469 469 HOH HOH . F 5 HOH A 105 470 470 HOH HOH . F 5 HOH A 106 471 471 HOH HOH . F 5 HOH A 107 472 472 HOH HOH . F 5 HOH A 108 473 473 HOH HOH . F 5 HOH A 109 474 474 HOH HOH . F 5 HOH A 110 476 476 HOH HOH . F 5 HOH A 111 477 477 HOH HOH . F 5 HOH A 112 478 478 HOH HOH . F 5 HOH A 113 479 479 HOH HOH . F 5 HOH A 114 480 480 HOH HOH . F 5 HOH A 115 481 481 HOH HOH . F 5 HOH A 116 482 482 HOH HOH . F 5 HOH A 117 483 483 HOH HOH . F 5 HOH A 118 484 484 HOH HOH . F 5 HOH A 119 485 485 HOH HOH . F 5 HOH A 120 487 487 HOH HOH . F 5 HOH A 121 488 488 HOH HOH . F 5 HOH A 122 489 489 HOH HOH . F 5 HOH A 123 490 490 HOH HOH . F 5 HOH A 124 491 491 HOH HOH . F 5 HOH A 125 497 497 HOH HOH . F 5 HOH A 126 499 499 HOH HOH . F 5 HOH A 127 501 501 HOH HOH . F 5 HOH A 128 502 502 HOH HOH . F 5 HOH A 129 503 503 HOH HOH . F 5 HOH A 130 504 504 HOH HOH . F 5 HOH A 131 506 506 HOH HOH . F 5 HOH A 132 507 507 HOH HOH . F 5 HOH A 133 508 508 HOH HOH . F 5 HOH A 134 509 509 HOH HOH . F 5 HOH A 135 510 510 HOH HOH . F 5 HOH A 136 511 511 HOH HOH . F 5 HOH A 137 513 513 HOH HOH . F 5 HOH A 138 514 514 HOH HOH . F 5 HOH A 139 515 515 HOH HOH . F 5 HOH A 140 516 516 HOH HOH . F 5 HOH A 141 517 517 HOH HOH . F 5 HOH A 142 518 518 HOH HOH . F 5 HOH A 143 520 520 HOH HOH . F 5 HOH A 144 521 521 HOH HOH . F 5 HOH A 145 522 522 HOH HOH . F 5 HOH A 146 523 523 HOH HOH . F 5 HOH A 147 524 524 HOH HOH . F 5 HOH A 148 528 528 HOH HOH . F 5 HOH A 149 529 529 HOH HOH . F 5 HOH A 150 531 531 HOH HOH . F 5 HOH A 151 532 532 HOH HOH . F 5 HOH A 152 534 534 HOH HOH . F 5 HOH A 153 535 535 HOH HOH . F 5 HOH A 154 536 536 HOH HOH . F 5 HOH A 155 537 537 HOH HOH . F 5 HOH A 156 538 538 HOH HOH . F 5 HOH A 157 539 539 HOH HOH . F 5 HOH A 158 540 540 HOH HOH . F 5 HOH A 159 548 548 HOH HOH . F 5 HOH A 160 549 549 HOH HOH . F 5 HOH A 161 550 550 HOH HOH . F 5 HOH A 162 551 551 HOH HOH . F 5 HOH A 163 552 552 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 N N SMM . . . D 4 -40.396 -2.143 76.018 1 45.8 ? N SMM 368 A 1 HETATM 2 C CA SMM . . . D 4 -39.325 -1.206 76.019 1 46.7 ? CA SMM 368 A 1 HETATM 3 C CB SMM . . . D 4 -38.632 -1.317 74.691 1 46.71 ? CB SMM 368 A 1 HETATM 4 C CG SMM . . . D 4 -37.02 -1.489 74.902 1 46.92 ? CG SMM 368 A 1 HETATM 5 S SD SMM . . . D 4 -36.219 -1.279 73.45 1 47.8 ? SD SMM 368 A 1 HETATM 6 C CE SMM . . . D 4 -36.055 -2.618 72.798 1 45.65 ? CE SMM 368 A 1 HETATM 7 C C5' SMM . . . D 4 -34.714 -0.581 73.753 1 44.02 ? C5' SMM 368 A 1 HETATM 8 C C4' SMM . . . D 4 -33.904 -0.343 72.495 1 42.4 ? C4' SMM 368 A 1 HETATM 9 O O4' SMM . . . D 4 -34.763 0.237 71.473 1 42.34 ? O4' SMM 368 A 1 HETATM 10 C C1' SMM . . . D 4 -34.242 1.493 71.063 1 41.48 ? C1' SMM 368 A 1 HETATM 11 N N9 SMM . . . D 4 -35.376 2.364 70.766 1 42.26 ? N9 SMM 368 A 1 HETATM 12 C C4 SMM . . . D 4 -36.423 2.641 71.616 1 42.72 ? C4 SMM 368 A 1 HETATM 13 N N3 SMM . . . D 4 -36.606 2.173 72.871 1 42.05 ? N3 SMM 368 A 1 HETATM 14 C C2 SMM . . . D 4 -37.735 2.646 73.402 1 42.49 ? C2 SMM 368 A 1 HETATM 15 N N1 SMM . . . D 4 -38.641 3.477 72.858 1 42.33 ? N1 SMM 368 A 1 HETATM 16 C C6 SMM . . . D 4 -38.431 3.933 71.592 1 42.85 ? C6 SMM 368 A 1 HETATM 17 N N6 SMM . . . D 4 -39.337 4.759 71.055 1 42.82 ? N6 SMM 368 A 1 HETATM 18 C C5 SMM . . . D 4 -37.26 3.499 70.917 1 42.27 ? C5 SMM 368 A 1 HETATM 19 N N7 SMM . . . D 4 -36.75 3.762 69.653 1 42.85 ? N7 SMM 368 A 1 HETATM 20 C C8 SMM . . . D 4 -35.635 3.069 69.611 1 42.63 ? C8 SMM 368 A 1 HETATM 21 C C2' SMM . . . D 4 -33.381 1.962 72.227 1 40.97 ? C2' SMM 368 A 1 HETATM 22 O O2' SMM . . . D 4 -32.465 2.969 71.837 1 41.1 ? O2' SMM 368 A 1 HETATM 23 C C3' SMM . . . D 4 -32.757 0.653 72.687 1 41.2 ? C3' SMM 368 A 1 HETATM 24 O O3' SMM . . . D 4 -31.668 0.308 71.829 1 39.17 ? O3' SMM 368 A 1 HETATM 25 C C SMM . . . D 4 -39.834 0.243 76.193 1 47.89 ? C SMM 368 A 1 HETATM 26 O O SMM . . . D 4 -39.544 1.098 75.319 1 49.64 ? O SMM 368 A 1 HETATM 27 O OXT SMM . . . D 4 -40.519 0.5 77.211 1 47.93 ? OXT SMM 368 A 1 HETATM 28 C CXT SMM . . . D 4 -39.827 0.899 78.254 1 46.59 ? CXT SMM 368 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #