data_3EP6
#
_model_server_result.job_id            AGm7ZDwxtm7pEk3jPdaAFQ 
_model_server_result.datetime_utc      '2024-11-13 09:32:04' 
_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          3ep6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":368}' 
#
_entry.id    3EP6 
#
_exptl.entry_id    3EP6 
_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          104.95 
_cell.angle_gamma         90 
_cell.entry_id            3EP6 
_cell.length_a            99.219 
_cell.length_b            50.598 
_cell.length_c            68.824 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EP6 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? 
#
_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                     3EP6 
_atom_sites.fract_transf_matrix[1][1]    0.010079 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002691 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019764 
_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]    0.015039 
_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 2 337 337 HOH HOH . 
E 5 HOH B 3 339 339 HOH HOH . 
E 5 HOH B 4 343 343 HOH HOH . 
E 5 HOH B 5 357 357 HOH HOH . 
E 5 HOH B 6 361 361 HOH HOH . 
E 5 HOH B 7 362 362 HOH HOH . 
E 5 HOH B 8 373 373 HOH HOH . 
E 5 HOH B 9 374 374 HOH HOH . 
E 5 HOH B 10 375 375 HOH HOH . 
E 5 HOH B 11 378 378 HOH HOH . 
E 5 HOH B 12 387 387 HOH HOH . 
E 5 HOH B 13 388 388 HOH HOH . 
E 5 HOH B 14 391 391 HOH HOH . 
E 5 HOH B 15 392 392 HOH HOH . 
E 5 HOH B 16 393 393 HOH HOH . 
E 5 HOH B 17 396 396 HOH HOH . 
E 5 HOH B 18 397 397 HOH HOH . 
E 5 HOH B 19 410 410 HOH HOH . 
E 5 HOH B 20 411 411 HOH HOH . 
E 5 HOH B 21 414 414 HOH HOH . 
E 5 HOH B 22 416 416 HOH HOH . 
E 5 HOH B 23 417 417 HOH HOH . 
E 5 HOH B 24 418 418 HOH HOH . 
E 5 HOH B 25 421 421 HOH HOH . 
E 5 HOH B 26 427 427 HOH HOH . 
E 5 HOH B 27 430 430 HOH HOH . 
E 5 HOH B 28 435 435 HOH HOH . 
E 5 HOH B 29 442 442 HOH HOH . 
E 5 HOH B 30 454 454 HOH HOH . 
E 5 HOH B 31 459 459 HOH HOH . 
E 5 HOH B 32 460 460 HOH HOH . 
E 5 HOH B 33 469 469 HOH HOH . 
E 5 HOH B 34 472 472 HOH HOH . 
E 5 HOH B 35 474 474 HOH HOH . 
E 5 HOH B 36 475 475 HOH HOH . 
E 5 HOH B 37 476 476 HOH HOH . 
E 5 HOH B 38 480 480 HOH HOH . 
E 5 HOH B 39 481 481 HOH HOH . 
E 5 HOH B 40 488 488 HOH HOH . 
E 5 HOH B 41 489 489 HOH HOH . 
E 5 HOH B 42 490 490 HOH HOH . 
E 5 HOH B 43 492 492 HOH HOH . 
E 5 HOH B 44 493 493 HOH HOH . 
F 5 HOH A 1 329 329 HOH HOH . 
F 5 HOH A 2 331 331 HOH HOH . 
F 5 HOH A 3 332 332 HOH HOH . 
F 5 HOH A 4 333 333 HOH HOH . 
F 5 HOH A 5 334 334 HOH HOH . 
F 5 HOH A 6 335 335 HOH HOH . 
F 5 HOH A 7 336 336 HOH HOH . 
F 5 HOH A 8 338 338 HOH HOH . 
F 5 HOH A 9 340 340 HOH HOH . 
F 5 HOH A 10 341 341 HOH HOH . 
F 5 HOH A 11 342 342 HOH HOH . 
F 5 HOH A 12 344 344 HOH HOH . 
F 5 HOH A 13 345 345 HOH HOH . 
F 5 HOH A 14 346 346 HOH HOH . 
F 5 HOH A 15 347 347 HOH HOH . 
F 5 HOH A 16 349 349 HOH HOH . 
F 5 HOH A 17 350 350 HOH HOH . 
F 5 HOH A 18 351 351 HOH HOH . 
F 5 HOH A 19 352 352 HOH HOH . 
F 5 HOH A 20 353 353 HOH HOH . 
F 5 HOH A 21 354 354 HOH HOH . 
F 5 HOH A 22 355 355 HOH HOH . 
F 5 HOH A 23 356 356 HOH HOH . 
F 5 HOH A 24 358 358 HOH HOH . 
F 5 HOH A 25 359 359 HOH HOH . 
F 5 HOH A 26 360 360 HOH HOH . 
F 5 HOH A 27 363 363 HOH HOH . 
F 5 HOH A 28 364 364 HOH HOH . 
F 5 HOH A 29 365 365 HOH HOH . 
F 5 HOH A 30 366 366 HOH HOH . 
F 5 HOH A 31 367 367 HOH HOH . 
F 5 HOH A 32 369 369 HOH HOH . 
F 5 HOH A 33 370 370 HOH HOH . 
F 5 HOH A 34 371 371 HOH HOH . 
F 5 HOH A 35 372 372 HOH HOH . 
F 5 HOH A 36 376 376 HOH HOH . 
F 5 HOH A 37 377 377 HOH HOH . 
F 5 HOH A 38 379 379 HOH HOH . 
F 5 HOH A 39 380 380 HOH HOH . 
F 5 HOH A 40 381 381 HOH HOH . 
F 5 HOH A 41 382 382 HOH HOH . 
F 5 HOH A 42 383 383 HOH HOH . 
F 5 HOH A 43 385 385 HOH HOH . 
F 5 HOH A 44 386 386 HOH HOH . 
F 5 HOH A 45 389 389 HOH HOH . 
F 5 HOH A 46 390 390 HOH HOH . 
F 5 HOH A 47 394 394 HOH HOH . 
F 5 HOH A 48 395 395 HOH HOH . 
F 5 HOH A 49 398 398 HOH HOH . 
F 5 HOH A 50 399 399 HOH HOH . 
F 5 HOH A 51 402 402 HOH HOH . 
F 5 HOH A 52 403 403 HOH HOH . 
F 5 HOH A 53 404 404 HOH HOH . 
F 5 HOH A 54 405 405 HOH HOH . 
F 5 HOH A 55 406 406 HOH HOH . 
F 5 HOH A 56 407 407 HOH HOH . 
F 5 HOH A 57 408 408 HOH HOH . 
F 5 HOH A 58 409 409 HOH HOH . 
F 5 HOH A 59 412 412 HOH HOH . 
F 5 HOH A 60 413 413 HOH HOH . 
F 5 HOH A 61 415 415 HOH HOH . 
F 5 HOH A 62 419 419 HOH HOH . 
F 5 HOH A 63 420 420 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 68 428 428 HOH HOH . 
F 5 HOH A 69 429 429 HOH HOH . 
F 5 HOH A 70 432 432 HOH HOH . 
F 5 HOH A 71 433 433 HOH HOH . 
F 5 HOH A 72 434 434 HOH HOH . 
F 5 HOH A 73 436 436 HOH HOH . 
F 5 HOH A 74 437 437 HOH HOH . 
F 5 HOH A 75 438 438 HOH HOH . 
F 5 HOH A 76 439 439 HOH HOH . 
F 5 HOH A 77 440 440 HOH HOH . 
F 5 HOH A 78 441 441 HOH HOH . 
F 5 HOH A 79 443 443 HOH HOH . 
F 5 HOH A 80 444 444 HOH HOH . 
F 5 HOH A 81 447 447 HOH HOH . 
F 5 HOH A 82 448 448 HOH HOH . 
F 5 HOH A 83 449 449 HOH HOH . 
F 5 HOH A 84 450 450 HOH HOH . 
F 5 HOH A 85 451 451 HOH HOH . 
F 5 HOH A 86 453 453 HOH HOH . 
F 5 HOH A 87 455 455 HOH HOH . 
F 5 HOH A 88 456 456 HOH HOH . 
F 5 HOH A 89 457 457 HOH HOH . 
F 5 HOH A 90 458 458 HOH HOH . 
F 5 HOH A 91 461 461 HOH HOH . 
F 5 HOH A 92 462 462 HOH HOH . 
F 5 HOH A 93 463 463 HOH HOH . 
F 5 HOH A 94 464 464 HOH HOH . 
F 5 HOH A 95 465 465 HOH HOH . 
F 5 HOH A 96 466 466 HOH HOH . 
F 5 HOH A 97 468 468 HOH HOH . 
F 5 HOH A 98 470 470 HOH HOH . 
F 5 HOH A 99 473 473 HOH HOH . 
F 5 HOH A 100 477 477 HOH HOH . 
F 5 HOH A 101 479 479 HOH HOH . 
F 5 HOH A 102 482 482 HOH HOH . 
F 5 HOH A 103 483 483 HOH HOH . 
F 5 HOH A 104 484 484 HOH HOH . 
F 5 HOH A 105 485 485 HOH HOH . 
F 5 HOH A 106 486 486 HOH HOH . 
F 5 HOH A 107 487 487 HOH HOH . 
F 5 HOH A 108 494 494 HOH HOH . 
F 5 HOH A 109 495 495 HOH HOH . 
F 5 HOH A 110 496 496 HOH HOH . 
F 5 HOH A 111 497 497 HOH HOH . 
F 5 HOH A 112 498 498 HOH HOH . 
F 5 HOH A 113 499 499 HOH HOH . 
F 5 HOH A 114 500 500 HOH HOH . 
F 5 HOH A 115 501 501 HOH HOH . 
F 5 HOH A 116 502 502 HOH HOH . 
F 5 HOH A 117 503 503 HOH HOH . 
F 5 HOH A 118 504 504 HOH HOH . 
F 5 HOH A 119 505 505 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 -21.791 -9.42 9.524 1 36.64 ? N SMM 368 A 1 
HETATM 2 C CA SMM . . . D 4 -20.728 -8.473 9.514 1 38.89 ? CA SMM 368 A 1 
HETATM 3 C CB SMM . . . D 4 -20.033 -8.594 8.188 1 38.66 ? CB SMM 368 A 1 
HETATM 4 C CG SMM . . . D 4 -18.42 -8.749 8.402 1 38.94 ? CG SMM 368 A 1 
HETATM 5 S SD SMM . . . D 4 -17.62 -8.549 6.948 1 38.72 ? SD SMM 368 A 1 
HETATM 6 C CE SMM . . . D 4 -17.444 -9.894 6.312 1 37.32 ? CE SMM 368 A 1 
HETATM 7 C C5' SMM . . . D 4 -16.121 -7.835 7.244 1 32.37 ? C5' SMM 368 A 1 
HETATM 8 C C4' SMM . . . D 4 -15.312 -7.604 5.983 1 30.44 ? C4' SMM 368 A 1 
HETATM 9 O O4' SMM . . . D 4 -16.176 -7.044 4.954 1 28.54 ? O4' SMM 368 A 1 
HETATM 10 C C1' SMM . . . D 4 -15.665 -5.788 4.53 1 28.53 ? C1' SMM 368 A 1 
HETATM 11 N N9 SMM . . . D 4 -16.807 -4.93 4.222 1 28.01 ? N9 SMM 368 A 1 
HETATM 12 C C4 SMM . . . D 4 -17.857 -4.653 5.068 1 29.82 ? C4 SMM 368 A 1 
HETATM 13 N N3 SMM . . . D 4 -18.036 -5.108 6.329 1 28.18 ? N3 SMM 368 A 1 
HETATM 14 C C2 SMM . . . D 4 -19.17 -4.638 6.854 1 29.79 ? C2 SMM 368 A 1 
HETATM 15 N N1 SMM . . . D 4 -20.083 -3.822 6.299 1 29.34 ? N1 SMM 368 A 1 
HETATM 16 C C6 SMM . . . D 4 -19.876 -3.379 5.028 1 29.1 ? C6 SMM 368 A 1 
HETATM 17 N N6 SMM . . . D 4 -20.789 -2.567 4.481 1 30.73 ? N6 SMM 368 A 1 
HETATM 18 C C5 SMM . . . D 4 -18.701 -3.81 4.359 1 28.26 ? C5 SMM 368 A 1 
HETATM 19 N N7 SMM . . . D 4 -18.192 -3.558 3.092 1 28.92 ? N7 SMM 368 A 1 
HETATM 20 C C8 SMM . . . D 4 -17.071 -4.241 3.059 1 28.79 ? C8 SMM 368 A 1 
HETATM 21 C C2' SMM . . . D 4 -14.809 -5.298 5.689 1 27.18 ? C2' SMM 368 A 1 
HETATM 22 O O2' SMM . . . D 4 -13.902 -4.288 5.288 1 29.25 ? O2' SMM 368 A 1 
HETATM 23 C C3' SMM . . . D 4 -14.174 -6.596 6.164 1 28.97 ? C3' SMM 368 A 1 
HETATM 24 O O3' SMM . . . D 4 -13.082 -6.942 5.311 1 28.88 ? O3' SMM 368 A 1 
HETATM 25 C C SMM . . . D 4 -21.25 -7.027 9.671 1 40.39 ? C SMM 368 A 1 
HETATM 26 O O SMM . . . D 4 -20.966 -6.18 8.787 1 43.41 ? O SMM 368 A 1 
HETATM 27 O OXT SMM . . . D 4 -21.937 -6.764 10.686 1 41.21 ? OXT SMM 368 A 1 
HETATM 28 C CXT SMM . . . D 4 -21.25 -6.347 11.724 1 39.51 ? CXT SMM 368 A 1 
#
_model_server_stats.io_time_ms              51 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#