data_4DCM
#
_model_server_result.job_id            4CdK7qwq8NrK_krWCqBopg 
_model_server_result.datetime_utc      '2025-03-13 17:24:43' 
_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          4dcm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    4DCM 
#
_exptl.entry_id    4DCM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              398.437 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYLMETHIONINE 
_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          104.46 
_cell.angle_gamma         90 
_cell.entry_id            4DCM 
_cell.length_a            67.185 
_cell.length_b            42.134 
_cell.length_c            72.429 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DCM 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                      2 
_struct_asym.id                             B 
_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 A C MSE 2 A MSE 8 1_555 A N ARG 3 A ARG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C PHE 214 A PHE 220 1_555 A N MSE 215 A MSE 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale3 A C MSE 215 A MSE 221 1_555 A N GLN 216 A GLN 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 A C PRO 256 A PRO 262 1_555 A N MSE 257 A MSE 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale5 A C MSE 257 A MSE 263 1_555 A N ALA 258 A ALA 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale6 A C ASN 269 A ASN 275 1_555 A N MSE 270 A MSE 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale7 A C MSE 270 A MSE 276 1_555 A N PRO 271 A PRO 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? 
covale ? covale8 A C PHE 279 A PHE 285 1_555 A N MSE 280 A MSE 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale9 A C MSE 280 A MSE 286 1_555 A N ILE 281 A ILE 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale10 A C GLU 315 A GLU 321 1_555 A N MSE 316 A MSE 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale11 A C MSE 316 A MSE 322 1_555 A N PHE 317 A PHE 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
#
_chem_comp.formula           'C15 H22 N6 O5 S' 
_chem_comp.formula_weight    398.437 
_chem_comp.id                SAM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-ADENOSYLMETHIONINE 
_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 SAM sing 293 n n 
N HN1 SAM sing 294 n n 
N HN2 SAM sing 295 n n 
CA C SAM sing 296 n n 
CA CB SAM sing 297 n n 
CA HA SAM sing 298 n n 
C O SAM doub 299 n n 
C OXT SAM sing 300 n n 
CB CG SAM sing 301 n n 
CB HB1 SAM sing 302 n n 
CB HB2 SAM sing 303 n n 
CG SD SAM sing 304 n n 
CG HG1 SAM sing 305 n n 
CG HG2 SAM sing 306 n n 
SD CE SAM sing 307 n n 
SD C5' SAM sing 308 n n 
CE HE1 SAM sing 309 n n 
CE HE2 SAM sing 310 n n 
CE HE3 SAM sing 311 n n 
C5' C4' SAM sing 312 n n 
C5' "H5'1" SAM sing 313 n n 
C5' "H5'2" SAM sing 314 n n 
C4' O4' SAM sing 315 n n 
C4' C3' SAM sing 316 n n 
C4' H4' SAM sing 317 n n 
O4' C1' SAM sing 318 n n 
C3' O3' SAM sing 319 n n 
C3' C2' SAM sing 320 n n 
C3' H3' SAM sing 321 n n 
O3' HO3' SAM sing 322 n n 
C2' O2' SAM sing 323 n n 
C2' C1' SAM sing 324 n n 
C2' H2' SAM sing 325 n n 
O2' HO2' SAM sing 326 n n 
C1' N9 SAM sing 327 n n 
C1' H1' SAM sing 328 n n 
N9 C8 SAM sing 329 n y 
N9 C4 SAM sing 330 n y 
C8 N7 SAM doub 331 n y 
C8 H8 SAM sing 332 n n 
N7 C5 SAM sing 333 n y 
C5 C6 SAM sing 334 n y 
C5 C4 SAM doub 335 n y 
C6 N6 SAM sing 336 n n 
C6 N1 SAM doub 337 n y 
N6 HN61 SAM sing 338 n n 
N6 HN62 SAM sing 339 n n 
N1 C2 SAM sing 340 n y 
C2 N3 SAM doub 341 n y 
C2 H2 SAM sing 342 n n 
N3 C4 SAM sing 343 n y 
#
_atom_sites.entry_id                     4DCM 
_atom_sites.fract_transf_matrix[1][1]    0.014884 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003838 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023734 
_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]    0.014258 
_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
B 2 SAM A 1 401 1 SAM SAM . 
C 3 PEG A 1 402 1 PEG PEG . 
D 3 PEG A 1 403 2 PEG PEG . 
E 4 HOH A 1 501 2 HOH HOH . 
E 4 HOH A 2 502 3 HOH HOH . 
E 4 HOH A 3 503 4 HOH HOH . 
E 4 HOH A 4 504 5 HOH HOH . 
E 4 HOH A 5 505 6 HOH HOH . 
E 4 HOH A 6 506 7 HOH HOH . 
E 4 HOH A 7 507 8 HOH HOH . 
E 4 HOH A 8 508 10 HOH HOH . 
E 4 HOH A 9 509 11 HOH HOH . 
E 4 HOH A 10 510 12 HOH HOH . 
E 4 HOH A 11 511 13 HOH HOH . 
E 4 HOH A 12 512 14 HOH HOH . 
E 4 HOH A 13 513 15 HOH HOH . 
E 4 HOH A 14 514 16 HOH HOH . 
E 4 HOH A 15 515 17 HOH HOH . 
E 4 HOH A 16 516 18 HOH HOH . 
E 4 HOH A 17 517 19 HOH HOH . 
E 4 HOH A 18 518 20 HOH HOH . 
E 4 HOH A 19 519 21 HOH HOH . 
E 4 HOH A 20 520 22 HOH HOH . 
E 4 HOH A 21 521 23 HOH HOH . 
E 4 HOH A 22 522 24 HOH HOH . 
E 4 HOH A 23 523 25 HOH HOH . 
E 4 HOH A 24 524 26 HOH HOH . 
E 4 HOH A 25 525 27 HOH HOH . 
E 4 HOH A 26 526 28 HOH HOH . 
E 4 HOH A 27 527 29 HOH HOH . 
E 4 HOH A 28 528 30 HOH HOH . 
E 4 HOH A 29 529 31 HOH HOH . 
E 4 HOH A 30 530 32 HOH HOH . 
E 4 HOH A 31 531 33 HOH HOH . 
E 4 HOH A 32 532 34 HOH HOH . 
E 4 HOH A 33 533 35 HOH HOH . 
E 4 HOH A 34 534 36 HOH HOH . 
E 4 HOH A 35 535 37 HOH HOH . 
E 4 HOH A 36 536 38 HOH HOH . 
E 4 HOH A 37 537 39 HOH HOH . 
E 4 HOH A 38 538 40 HOH HOH . 
E 4 HOH A 39 539 41 HOH HOH . 
E 4 HOH A 40 540 42 HOH HOH . 
E 4 HOH A 41 541 43 HOH HOH . 
E 4 HOH A 42 542 44 HOH HOH . 
E 4 HOH A 43 543 45 HOH HOH . 
E 4 HOH A 44 544 46 HOH HOH . 
E 4 HOH A 45 545 47 HOH HOH . 
E 4 HOH A 46 546 48 HOH HOH . 
E 4 HOH A 47 547 49 HOH HOH . 
E 4 HOH A 48 548 50 HOH HOH . 
E 4 HOH A 49 549 51 HOH HOH . 
E 4 HOH A 50 550 52 HOH HOH . 
E 4 HOH A 51 551 53 HOH HOH . 
E 4 HOH A 52 552 54 HOH HOH . 
E 4 HOH A 53 553 55 HOH HOH . 
E 4 HOH A 54 554 56 HOH HOH . 
E 4 HOH A 55 555 57 HOH HOH . 
E 4 HOH A 56 556 58 HOH HOH . 
E 4 HOH A 57 557 59 HOH HOH . 
E 4 HOH A 58 558 60 HOH HOH . 
E 4 HOH A 59 559 61 HOH HOH . 
E 4 HOH A 60 560 62 HOH HOH . 
E 4 HOH A 61 561 63 HOH HOH . 
E 4 HOH A 62 562 64 HOH HOH . 
E 4 HOH A 63 563 65 HOH HOH . 
E 4 HOH A 64 564 66 HOH HOH . 
E 4 HOH A 65 565 67 HOH HOH . 
E 4 HOH A 66 566 68 HOH HOH . 
E 4 HOH A 67 567 69 HOH HOH . 
E 4 HOH A 68 568 70 HOH HOH . 
E 4 HOH A 69 569 71 HOH HOH . 
E 4 HOH A 70 570 72 HOH HOH . 
E 4 HOH A 71 571 73 HOH HOH . 
E 4 HOH A 72 572 74 HOH HOH . 
E 4 HOH A 73 573 75 HOH HOH . 
E 4 HOH A 74 574 76 HOH HOH . 
E 4 HOH A 75 575 77 HOH HOH . 
E 4 HOH A 76 576 78 HOH HOH . 
E 4 HOH A 77 577 79 HOH HOH . 
E 4 HOH A 78 578 80 HOH HOH . 
E 4 HOH A 79 579 81 HOH HOH . 
E 4 HOH A 80 580 82 HOH HOH . 
E 4 HOH A 81 581 83 HOH HOH . 
E 4 HOH A 82 582 84 HOH HOH . 
E 4 HOH A 83 583 85 HOH HOH . 
E 4 HOH A 84 584 86 HOH HOH . 
E 4 HOH A 85 585 87 HOH HOH . 
E 4 HOH A 86 586 88 HOH HOH . 
E 4 HOH A 87 587 89 HOH HOH . 
E 4 HOH A 88 588 90 HOH HOH . 
E 4 HOH A 89 589 91 HOH HOH . 
E 4 HOH A 90 590 92 HOH HOH . 
E 4 HOH A 91 591 93 HOH HOH . 
E 4 HOH A 92 592 94 HOH HOH . 
E 4 HOH A 93 593 95 HOH HOH . 
E 4 HOH A 94 594 96 HOH HOH . 
E 4 HOH A 95 595 97 HOH HOH . 
E 4 HOH A 96 596 98 HOH HOH . 
E 4 HOH A 97 597 99 HOH HOH . 
E 4 HOH A 98 598 100 HOH HOH . 
E 4 HOH A 99 599 101 HOH HOH . 
E 4 HOH A 100 600 102 HOH HOH . 
E 4 HOH A 101 601 103 HOH HOH . 
E 4 HOH A 102 602 104 HOH HOH . 
E 4 HOH A 103 603 105 HOH HOH . 
E 4 HOH A 104 604 106 HOH HOH . 
E 4 HOH A 105 605 107 HOH HOH . 
E 4 HOH A 106 606 108 HOH HOH . 
E 4 HOH A 107 607 109 HOH HOH . 
E 4 HOH A 108 608 110 HOH HOH . 
E 4 HOH A 109 609 111 HOH HOH . 
E 4 HOH A 110 610 112 HOH HOH . 
E 4 HOH A 111 611 113 HOH HOH . 
E 4 HOH A 112 612 114 HOH HOH . 
E 4 HOH A 113 613 115 HOH HOH . 
E 4 HOH A 114 614 116 HOH HOH . 
E 4 HOH A 115 615 117 HOH HOH . 
E 4 HOH A 116 616 118 HOH HOH . 
E 4 HOH A 117 617 119 HOH HOH . 
E 4 HOH A 118 618 120 HOH HOH . 
E 4 HOH A 119 619 121 HOH HOH . 
E 4 HOH A 120 620 122 HOH HOH . 
E 4 HOH A 121 621 123 HOH HOH . 
E 4 HOH A 122 622 124 HOH HOH . 
E 4 HOH A 123 623 125 HOH HOH . 
E 4 HOH A 124 624 126 HOH HOH . 
E 4 HOH A 125 625 127 HOH HOH . 
E 4 HOH A 126 626 128 HOH HOH . 
E 4 HOH A 127 627 129 HOH HOH . 
E 4 HOH A 128 628 130 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 SAM . . . B 2 43.461 -5.396 45.92 1 33.73 ? N SAM 401 A 1 
HETATM 2 C CA SAM . . . B 2 43.083 -6.442 46.868 1 32.7 ? CA SAM 401 A 1 
HETATM 3 C C SAM . . . B 2 42.983 -7.792 46.169 1 35.56 ? C SAM 401 A 1 
HETATM 4 O O SAM . . . B 2 42.826 -8.828 46.818 1 37.74 ? O SAM 401 A 1 
HETATM 5 O OXT SAM . . . B 2 43.067 -7.872 44.94 1 31.95 ? OXT SAM 401 A 1 
HETATM 6 C CB SAM . . . B 2 41.774 -6.116 47.579 1 29.11 ? CB SAM 401 A 1 
HETATM 7 C CG SAM . . . B 2 40.538 -5.969 46.693 1 28.49 ? CG SAM 401 A 1 
HETATM 8 S SD SAM . . . B 2 39.006 -5.754 47.657 1 54.3 ? SD SAM 401 A 1 
HETATM 9 C CE SAM . . . B 2 37.866 -6.839 46.761 1 35.28 ? CE SAM 401 A 1 
HETATM 10 C C5' SAM . . . B 2 38.357 -4.147 47.112 1 34.36 ? C5' SAM 401 A 1 
HETATM 11 C C4' SAM . . . B 2 38.965 -2.96 47.854 1 29.36 ? C4' SAM 401 A 1 
HETATM 12 O O4' SAM . . . B 2 38.481 -1.733 47.34 1 25.9 ? O4' SAM 401 A 1 
HETATM 13 C C3' SAM . . . B 2 38.648 -2.961 49.341 1 26.62 ? C3' SAM 401 A 1 
HETATM 14 O O3' SAM . . . B 2 39.886 -2.979 50.019 1 24.07 ? O3' SAM 401 A 1 
HETATM 15 C C2' SAM . . . B 2 37.925 -1.647 49.588 1 24.44 ? C2' SAM 401 A 1 
HETATM 16 O O2' SAM . . . B 2 38.288 -1.034 50.808 1 23.19 ? O2' SAM 401 A 1 
HETATM 17 C C1' SAM . . . B 2 38.36 -0.808 48.398 1 23.56 ? C1' SAM 401 A 1 
HETATM 18 N N9 SAM . . . B 2 37.378 0.203 48.006 1 20.97 ? N9 SAM 401 A 1 
HETATM 19 C C8 SAM . . . B 2 36.012 0.087 48.053 1 22.96 ? C8 SAM 401 A 1 
HETATM 20 N N7 SAM . . . B 2 35.481 1.241 47.582 1 22.57 ? N7 SAM 401 A 1 
HETATM 21 C C5 SAM . . . B 2 36.485 2.084 47.242 1 22.67 ? C5 SAM 401 A 1 
HETATM 22 C C6 SAM . . . B 2 36.494 3.377 46.721 1 24.69 ? C6 SAM 401 A 1 
HETATM 23 N N6 SAM . . . B 2 35.353 4.017 46.463 1 28.63 ? N6 SAM 401 A 1 
HETATM 24 N N1 SAM . . . B 2 37.702 3.995 46.47 1 23.79 ? N1 SAM 401 A 1 
HETATM 25 C C2 SAM . . . B 2 38.885 3.336 46.736 1 22.42 ? C2 SAM 401 A 1 
HETATM 26 N N3 SAM . . . B 2 38.868 2.051 47.255 1 21 ? N3 SAM 401 A 1 
HETATM 27 C C4 SAM . . . B 2 37.687 1.438 47.505 1 20.86 ? C4 SAM 401 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#