data_3DZ3
#
_model_server_result.job_id            LR26ubfD_tqxHWkt1OVJlQ 
_model_server_result.datetime_utc      '2024-11-16 21:41:43' 
_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          3dz3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":368}' 
#
_entry.id    3DZ3 
#
_exptl.entry_id    3DZ3 
_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          104.52 
_cell.angle_gamma         90 
_cell.entry_id            3DZ3 
_cell.length_a            95.976 
_cell.length_b            44.245 
_cell.length_c            70.832 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DZ3 
_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 B C PYR 1 A PYR 68 1_555 B N SER 2 A SER 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? 
covale ? covale2 B CA PYR 1 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 316 n n 
N HN1 SMM sing 317 n n 
N HN2 SMM sing 318 n n 
CA CB SMM sing 319 n n 
CA C SMM sing 320 n n 
CA HA1 SMM sing 321 n n 
CB CG SMM sing 322 n n 
CB HB1 SMM sing 323 n n 
CB HB2 SMM sing 324 n n 
CG SD SMM sing 325 n n 
CG HG1 SMM sing 326 n n 
CG HG2 SMM sing 327 n n 
SD CE SMM sing 328 n n 
SD C5' SMM sing 329 n n 
SD HD1 SMM sing 330 n n 
CE HE1 SMM sing 331 n n 
CE HE2 SMM sing 332 n n 
CE HE3 SMM sing 333 n n 
C5' C4' SMM sing 334 n n 
C5' "H5'1" SMM sing 335 n n 
C5' "H5'2" SMM sing 336 n n 
C4' O4' SMM sing 337 n n 
C4' C3' SMM sing 338 n n 
C4' H4' SMM sing 339 n n 
O4' C1' SMM sing 340 n n 
C1' N9 SMM sing 341 n n 
C1' C2' SMM sing 342 n n 
C1' H1' SMM sing 343 n n 
N9 C4 SMM sing 344 n y 
N9 C8 SMM sing 345 n y 
C4 N3 SMM doub 346 n y 
C4 C5 SMM sing 347 n y 
N3 C2 SMM sing 348 n y 
C2 N1 SMM doub 349 n y 
C2 H2 SMM sing 350 n n 
N1 C6 SMM sing 351 n y 
C6 N6 SMM sing 352 n n 
C6 C5 SMM doub 353 n y 
N6 HN61 SMM sing 354 n n 
N6 HN62 SMM sing 355 n n 
C5 N7 SMM sing 356 n y 
N7 C8 SMM doub 357 n y 
C8 H8 SMM sing 358 n n 
C2' O2' SMM sing 359 n n 
C2' C3' SMM sing 360 n n 
C2' H2' SMM sing 361 n n 
O2' HO2' SMM sing 362 n n 
C3' O3' SMM sing 363 n n 
C3' H3' SMM sing 364 n n 
O3' HO3' SMM sing 365 n n 
C O SMM doub 366 n n 
C OXT SMM sing 367 n n 
OXT CXT SMM sing 368 n n 
CXT HXT1 SMM sing 369 n n 
CXT HXT2 SMM sing 370 n n 
CXT HXT3 SMM sing 371 n n 
#
_atom_sites.entry_id                     3DZ3 
_atom_sites.fract_transf_matrix[1][1]    0.010419 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002698 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022601 
_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]    0.014584 
_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 PUT B 1 350 350 PUT PUT . 
D 4 SMM A 1 368 368 SMM SMM . 
E 5 HOH B 1 351 2 HOH HOH . 
E 5 HOH B 2 352 4 HOH HOH . 
E 5 HOH B 3 353 12 HOH HOH . 
E 5 HOH B 4 354 20 HOH HOH . 
E 5 HOH B 5 355 21 HOH HOH . 
E 5 HOH B 6 356 26 HOH HOH . 
E 5 HOH B 7 357 28 HOH HOH . 
E 5 HOH B 8 359 33 HOH HOH . 
E 5 HOH B 9 360 37 HOH HOH . 
E 5 HOH B 10 361 39 HOH HOH . 
E 5 HOH B 11 362 44 HOH HOH . 
E 5 HOH B 12 363 45 HOH HOH . 
E 5 HOH B 13 364 46 HOH HOH . 
E 5 HOH B 14 365 48 HOH HOH . 
E 5 HOH B 15 366 52 HOH HOH . 
E 5 HOH B 16 367 54 HOH HOH . 
E 5 HOH B 17 368 55 HOH HOH . 
E 5 HOH B 18 369 56 HOH HOH . 
E 5 HOH B 19 370 60 HOH HOH . 
E 5 HOH B 20 371 63 HOH HOH . 
E 5 HOH B 21 372 70 HOH HOH . 
E 5 HOH B 22 373 79 HOH HOH . 
F 5 HOH A 1 358 30 HOH HOH . 
F 5 HOH A 2 369 1 HOH HOH . 
F 5 HOH A 3 370 3 HOH HOH . 
F 5 HOH A 4 371 5 HOH HOH . 
F 5 HOH A 5 372 6 HOH HOH . 
F 5 HOH A 6 373 7 HOH HOH . 
F 5 HOH A 7 374 8 HOH HOH . 
F 5 HOH A 8 375 9 HOH HOH . 
F 5 HOH A 9 376 10 HOH HOH . 
F 5 HOH A 10 377 11 HOH HOH . 
F 5 HOH A 11 378 13 HOH HOH . 
F 5 HOH A 12 379 14 HOH HOH . 
F 5 HOH A 13 380 15 HOH HOH . 
F 5 HOH A 14 381 16 HOH HOH . 
F 5 HOH A 15 382 17 HOH HOH . 
F 5 HOH A 16 383 18 HOH HOH . 
F 5 HOH A 17 384 19 HOH HOH . 
F 5 HOH A 18 385 22 HOH HOH . 
F 5 HOH A 19 386 23 HOH HOH . 
F 5 HOH A 20 387 24 HOH HOH . 
F 5 HOH A 21 388 25 HOH HOH . 
F 5 HOH A 22 389 27 HOH HOH . 
F 5 HOH A 23 390 29 HOH HOH . 
F 5 HOH A 24 391 31 HOH HOH . 
F 5 HOH A 25 392 32 HOH HOH . 
F 5 HOH A 26 393 34 HOH HOH . 
F 5 HOH A 27 394 35 HOH HOH . 
F 5 HOH A 28 395 36 HOH HOH . 
F 5 HOH A 29 396 38 HOH HOH . 
F 5 HOH A 30 397 40 HOH HOH . 
F 5 HOH A 31 398 41 HOH HOH . 
F 5 HOH A 32 399 42 HOH HOH . 
F 5 HOH A 33 400 43 HOH HOH . 
F 5 HOH A 34 401 47 HOH HOH . 
F 5 HOH A 35 402 49 HOH HOH . 
F 5 HOH A 36 403 50 HOH HOH . 
F 5 HOH A 37 404 51 HOH HOH . 
F 5 HOH A 38 405 53 HOH HOH . 
F 5 HOH A 39 406 57 HOH HOH . 
F 5 HOH A 40 407 58 HOH HOH . 
F 5 HOH A 41 408 59 HOH HOH . 
F 5 HOH A 42 409 61 HOH HOH . 
F 5 HOH A 43 410 62 HOH HOH . 
F 5 HOH A 44 411 64 HOH HOH . 
F 5 HOH A 45 412 65 HOH HOH . 
F 5 HOH A 46 413 66 HOH HOH . 
F 5 HOH A 47 414 67 HOH HOH . 
F 5 HOH A 48 415 68 HOH HOH . 
F 5 HOH A 49 416 69 HOH HOH . 
F 5 HOH A 50 417 71 HOH HOH . 
F 5 HOH A 51 418 72 HOH HOH . 
F 5 HOH A 52 419 73 HOH HOH . 
F 5 HOH A 53 420 74 HOH HOH . 
F 5 HOH A 54 421 75 HOH HOH . 
F 5 HOH A 55 422 76 HOH HOH . 
F 5 HOH A 56 423 77 HOH HOH . 
F 5 HOH A 57 424 78 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 26.84 -10.275 10.144 1 60.45 ? N SMM 368 A 1 
HETATM 2 C CA SMM . . . D 4 27.862 -9.274 10.194 1 60.55 ? CA SMM 368 A 1 
HETATM 3 C CB SMM . . . D 4 28.509 -9.208 8.84 1 58.61 ? CB SMM 368 A 1 
HETATM 4 C CG SMM . . . D 4 30.073 -9.684 8.937 1 58.28 ? CG SMM 368 A 1 
HETATM 5 S SD SMM . . . D 4 30.88 -9.38 7.501 1 56.99 ? SD SMM 368 A 1 
HETATM 6 C CE SMM . . . D 4 31.245 -10.678 6.858 1 57.2 ? CE SMM 368 A 1 
HETATM 7 C C5' SMM . . . D 4 32.262 -8.462 7.826 1 60.33 ? C5' SMM 368 A 1 
HETATM 8 C C4' SMM . . . D 4 33.081 -8.127 6.585 1 62.55 ? C4' SMM 368 A 1 
HETATM 9 O O4' SMM . . . D 4 32.235 -7.479 5.592 1 61.91 ? O4' SMM 368 A 1 
HETATM 10 C C1' SMM . . . D 4 32.766 -6.207 5.26 1 63.74 ? C1' SMM 368 A 1 
HETATM 11 N N9 SMM . . . D 4 31.635 -5.304 5.048 1 66.33 ? N9 SMM 368 A 1 
HETATM 12 C C4 SMM . . . D 4 30.507 -5.226 5.836 1 67.89 ? C4 SMM 368 A 1 
HETATM 13 N N3 SMM . . . D 4 30.224 -5.953 6.944 1 68.72 ? N3 SMM 368 A 1 
HETATM 14 C C2 SMM . . . D 4 29.033 -5.613 7.456 1 68.36 ? C2 SMM 368 A 1 
HETATM 15 N N1 SMM . . . D 4 28.158 -4.693 7.015 1 68.39 ? N1 SMM 368 A 1 
HETATM 16 C C6 SMM . . . D 4 28.471 -3.977 5.9 1 68.71 ? C6 SMM 368 A 1 
HETATM 17 N N6 SMM . . . D 4 27.597 -3.063 5.469 1 69.23 ? N6 SMM 368 A 1 
HETATM 18 C C5 SMM . . . D 4 29.711 -4.247 5.262 1 68.48 ? C5 SMM 368 A 1 
HETATM 19 N N7 SMM . . . D 4 30.328 -3.717 4.134 1 68.41 ? N7 SMM 368 A 1 
HETATM 20 C C8 SMM . . . D 4 31.461 -4.375 4.05 1 66.99 ? C8 SMM 368 A 1 
HETATM 21 C C2' SMM . . . D 4 33.669 -5.812 6.428 1 62.49 ? C2' SMM 368 A 1 
HETATM 22 O O2' SMM . . . D 4 34.634 -4.849 6.055 1 59.71 ? O2' SMM 368 A 1 
HETATM 23 C C3' SMM . . . D 4 34.238 -7.155 6.861 1 62.59 ? C3' SMM 368 A 1 
HETATM 24 O O3' SMM . . . D 4 35.365 -7.494 6.05 1 63.47 ? O3' SMM 368 A 1 
HETATM 25 C C SMM . . . D 4 27.305 -7.862 10.541 1 61.66 ? C SMM 368 A 1 
HETATM 26 O O SMM . . . D 4 28.134 -6.923 10.705 1 63.1 ? O SMM 368 A 1 
HETATM 27 O OXT SMM . . . D 4 26.048 -7.722 10.642 1 60.66 ? OXT SMM 368 A 1 
HETATM 28 C CXT SMM . . . D 4 25.64 -6.965 11.634 1 59.63 ? CXT SMM 368 A 1 
#
_model_server_stats.io_time_ms              123 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#