data_5CPR
#
_model_server_result.job_id            zLCv-_pCv6F9lrhKIaW4eA 
_model_server_result.datetime_utc      '2024-11-14 04:48:29' 
_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          5cpr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    5CPR 
#
_exptl.entry_id    5CPR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              398.437 
_entity.id                          3 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            5CPR 
_cell.length_a            42.209 
_cell.length_b            47.913 
_cell.length_c            129.072 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CPR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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                      3 
_struct_asym.id                             C 
_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
metalc ? metalc1 A SG CYS 208 B CYS 275 1_555 B ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc2 A SG CYS 252 B CYS 319 1_555 B ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc3 A SG CYS 254 B CYS 321 1_555 B ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc4 A SG CYS 257 B CYS 324 1_555 B ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
#
_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 320 n n 
N HN1 SAM sing 321 n n 
N HN2 SAM sing 322 n n 
CA C SAM sing 323 n n 
CA CB SAM sing 324 n n 
CA HA SAM sing 325 n n 
C O SAM doub 326 n n 
C OXT SAM sing 327 n n 
CB CG SAM sing 328 n n 
CB HB1 SAM sing 329 n n 
CB HB2 SAM sing 330 n n 
CG SD SAM sing 331 n n 
CG HG1 SAM sing 332 n n 
CG HG2 SAM sing 333 n n 
SD CE SAM sing 334 n n 
SD C5' SAM sing 335 n n 
CE HE1 SAM sing 336 n n 
CE HE2 SAM sing 337 n n 
CE HE3 SAM sing 338 n n 
C5' C4' SAM sing 339 n n 
C5' "H5'1" SAM sing 340 n n 
C5' "H5'2" SAM sing 341 n n 
C4' O4' SAM sing 342 n n 
C4' C3' SAM sing 343 n n 
C4' H4' SAM sing 344 n n 
O4' C1' SAM sing 345 n n 
C3' O3' SAM sing 346 n n 
C3' C2' SAM sing 347 n n 
C3' H3' SAM sing 348 n n 
O3' HO3' SAM sing 349 n n 
C2' O2' SAM sing 350 n n 
C2' C1' SAM sing 351 n n 
C2' H2' SAM sing 352 n n 
O2' HO2' SAM sing 353 n n 
C1' N9 SAM sing 354 n n 
C1' H1' SAM sing 355 n n 
N9 C8 SAM sing 356 n y 
N9 C4 SAM sing 357 n y 
C8 N7 SAM doub 358 n y 
C8 H8 SAM sing 359 n n 
N7 C5 SAM sing 360 n y 
C5 C6 SAM sing 361 n y 
C5 C4 SAM doub 362 n y 
C6 N6 SAM sing 363 n n 
C6 N1 SAM doub 364 n y 
N6 HN61 SAM sing 365 n n 
N6 HN62 SAM sing 366 n n 
N1 C2 SAM sing 367 n y 
C2 N3 SAM doub 368 n y 
C2 H2 SAM sing 369 n n 
N3 C4 SAM sing 370 n y 
#
_atom_sites.entry_id                     5CPR 
_atom_sites.fract_transf_matrix[1][1]    0.023692 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020871 
_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]    0.007748 
_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 ZN B 1 401 400 ZN ZN . 
C 3 SAM B 1 402 500 SAM SAM . 
D 4 539 B 1 403 1 539 LIG . 
E 5 HOH B 1 501 93 HOH HOH . 
E 5 HOH B 2 502 22 HOH HOH . 
E 5 HOH B 3 503 92 HOH HOH . 
E 5 HOH B 4 504 2 HOH HOH . 
E 5 HOH B 5 505 3 HOH HOH . 
E 5 HOH B 6 506 12 HOH HOH . 
E 5 HOH B 7 507 27 HOH HOH . 
E 5 HOH B 8 508 59 HOH HOH . 
E 5 HOH B 9 509 43 HOH HOH . 
E 5 HOH B 10 510 17 HOH HOH . 
E 5 HOH B 11 511 33 HOH HOH . 
E 5 HOH B 12 512 61 HOH HOH . 
E 5 HOH B 13 513 94 HOH HOH . 
E 5 HOH B 14 514 44 HOH HOH . 
E 5 HOH B 15 515 9 HOH HOH . 
E 5 HOH B 16 516 34 HOH HOH . 
E 5 HOH B 17 517 111 HOH HOH . 
E 5 HOH B 18 518 97 HOH HOH . 
E 5 HOH B 19 519 95 HOH HOH . 
E 5 HOH B 20 520 78 HOH HOH . 
E 5 HOH B 21 521 98 HOH HOH . 
E 5 HOH B 22 522 136 HOH HOH . 
E 5 HOH B 23 523 21 HOH HOH . 
E 5 HOH B 24 524 91 HOH HOH . 
E 5 HOH B 25 525 52 HOH HOH . 
E 5 HOH B 26 526 113 HOH HOH . 
E 5 HOH B 27 527 14 HOH HOH . 
E 5 HOH B 28 528 100 HOH HOH . 
E 5 HOH B 29 529 6 HOH HOH . 
E 5 HOH B 30 530 19 HOH HOH . 
E 5 HOH B 31 531 5 HOH HOH . 
E 5 HOH B 32 532 18 HOH HOH . 
E 5 HOH B 33 533 56 HOH HOH . 
E 5 HOH B 34 534 15 HOH HOH . 
E 5 HOH B 35 535 63 HOH HOH . 
E 5 HOH B 36 536 13 HOH HOH . 
E 5 HOH B 37 537 35 HOH HOH . 
E 5 HOH B 38 538 68 HOH HOH . 
E 5 HOH B 39 539 96 HOH HOH . 
E 5 HOH B 40 540 1 HOH HOH . 
E 5 HOH B 41 541 81 HOH HOH . 
E 5 HOH B 42 542 84 HOH HOH . 
E 5 HOH B 43 543 80 HOH HOH . 
E 5 HOH B 44 544 133 HOH HOH . 
E 5 HOH B 45 545 29 HOH HOH . 
E 5 HOH B 46 546 30 HOH HOH . 
E 5 HOH B 47 547 79 HOH HOH . 
E 5 HOH B 48 548 62 HOH HOH . 
E 5 HOH B 49 549 74 HOH HOH . 
E 5 HOH B 50 550 60 HOH HOH . 
E 5 HOH B 51 551 26 HOH HOH . 
E 5 HOH B 52 552 25 HOH HOH . 
E 5 HOH B 53 553 32 HOH HOH . 
E 5 HOH B 54 554 16 HOH HOH . 
E 5 HOH B 55 555 134 HOH HOH . 
E 5 HOH B 56 556 90 HOH HOH . 
E 5 HOH B 57 557 72 HOH HOH . 
E 5 HOH B 58 558 23 HOH HOH . 
E 5 HOH B 59 559 20 HOH HOH . 
E 5 HOH B 60 560 7 HOH HOH . 
E 5 HOH B 61 561 38 HOH HOH . 
E 5 HOH B 62 562 31 HOH HOH . 
E 5 HOH B 63 563 48 HOH HOH . 
E 5 HOH B 64 564 86 HOH HOH . 
E 5 HOH B 65 565 42 HOH HOH . 
E 5 HOH B 66 566 64 HOH HOH . 
E 5 HOH B 67 567 75 HOH HOH . 
E 5 HOH B 68 568 66 HOH HOH . 
E 5 HOH B 69 569 89 HOH HOH . 
E 5 HOH B 70 570 24 HOH HOH . 
E 5 HOH B 71 571 82 HOH HOH . 
E 5 HOH B 72 572 47 HOH HOH . 
E 5 HOH B 73 573 112 HOH HOH . 
E 5 HOH B 74 574 73 HOH HOH . 
E 5 HOH B 75 575 102 HOH HOH . 
E 5 HOH B 76 576 125 HOH HOH . 
E 5 HOH B 77 577 53 HOH HOH . 
E 5 HOH B 78 578 55 HOH HOH . 
E 5 HOH B 79 579 58 HOH HOH . 
E 5 HOH B 80 580 51 HOH HOH . 
E 5 HOH B 81 581 143 HOH HOH . 
E 5 HOH B 82 582 138 HOH HOH . 
E 5 HOH B 83 583 135 HOH HOH . 
E 5 HOH B 84 584 126 HOH HOH . 
E 5 HOH B 85 585 71 HOH HOH . 
E 5 HOH B 86 586 115 HOH HOH . 
E 5 HOH B 87 587 114 HOH HOH . 
E 5 HOH B 88 588 37 HOH HOH . 
E 5 HOH B 89 589 8 HOH HOH . 
E 5 HOH B 90 590 65 HOH HOH . 
E 5 HOH B 91 591 103 HOH HOH . 
E 5 HOH B 92 592 10 HOH HOH . 
E 5 HOH B 93 593 137 HOH HOH . 
E 5 HOH B 94 594 107 HOH HOH . 
E 5 HOH B 95 595 36 HOH HOH . 
E 5 HOH B 96 596 46 HOH HOH . 
E 5 HOH B 97 597 83 HOH HOH . 
E 5 HOH B 98 598 128 HOH HOH . 
E 5 HOH B 99 599 104 HOH HOH . 
E 5 HOH B 100 600 45 HOH HOH . 
E 5 HOH B 101 601 117 HOH HOH . 
E 5 HOH B 102 602 54 HOH HOH . 
E 5 HOH B 103 603 67 HOH HOH . 
E 5 HOH B 104 604 70 HOH HOH . 
E 5 HOH B 105 605 11 HOH HOH . 
E 5 HOH B 106 606 4 HOH HOH . 
E 5 HOH B 107 607 69 HOH HOH . 
E 5 HOH B 108 608 41 HOH HOH . 
E 5 HOH B 109 609 106 HOH HOH . 
E 5 HOH B 110 610 124 HOH HOH . 
E 5 HOH B 111 611 88 HOH HOH . 
E 5 HOH B 112 612 99 HOH HOH . 
E 5 HOH B 113 613 105 HOH HOH . 
E 5 HOH B 114 614 85 HOH HOH . 
E 5 HOH B 115 615 118 HOH HOH . 
E 5 HOH B 116 616 110 HOH HOH . 
E 5 HOH B 117 617 129 HOH HOH . 
E 5 HOH B 118 618 140 HOH HOH . 
E 5 HOH B 119 619 50 HOH HOH . 
E 5 HOH B 120 620 108 HOH HOH . 
E 5 HOH B 121 621 144 HOH HOH . 
E 5 HOH B 122 622 101 HOH HOH . 
E 5 HOH B 123 623 123 HOH HOH . 
E 5 HOH B 124 624 76 HOH HOH . 
E 5 HOH B 125 625 142 HOH HOH . 
E 5 HOH B 126 626 57 HOH HOH . 
E 5 HOH B 127 627 40 HOH HOH . 
E 5 HOH B 128 628 109 HOH HOH . 
E 5 HOH B 129 629 116 HOH HOH . 
E 5 HOH B 130 630 139 HOH HOH . 
E 5 HOH B 131 631 39 HOH HOH . 
E 5 HOH B 132 632 132 HOH HOH . 
E 5 HOH B 133 633 49 HOH HOH . 
E 5 HOH B 134 634 77 HOH HOH . 
E 5 HOH B 135 635 28 HOH HOH . 
E 5 HOH B 136 636 131 HOH HOH . 
E 5 HOH B 137 637 119 HOH HOH . 
E 5 HOH B 138 638 141 HOH HOH . 
E 5 HOH B 139 639 120 HOH HOH . 
E 5 HOH B 140 640 127 HOH HOH . 
E 5 HOH B 141 641 87 HOH HOH . 
E 5 HOH B 142 642 130 HOH HOH . 
E 5 HOH B 143 643 122 HOH HOH . 
E 5 HOH B 144 644 121 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 . . . C 3 -11.946 -5.537 25.041 1 19.9 ? N SAM 402 B 1 
HETATM 2 C CA SAM . . . C 3 -10.471 -5.477 25.074 1 22.13 ? CA SAM 402 B 1 
HETATM 3 C C SAM . . . C 3 -9.858 -4.349 24.24 1 25.76 ? C SAM 402 B 1 
HETATM 4 O O SAM . . . C 3 -10.617 -3.724 23.441 1 25.51 ? O SAM 402 B 1 
HETATM 5 O OXT SAM . . . C 3 -8.64 -4.132 24.482 1 27.93 ? OXT SAM 402 B 1 
HETATM 6 C CB SAM . . . C 3 -9.917 -6.775 24.494 1 23.6 ? CB SAM 402 B 1 
HETATM 7 C CG SAM . . . C 3 -9.613 -7.835 25.545 1 22.31 ? CG SAM 402 B 1 
HETATM 8 S SD SAM . . . C 3 -8.125 -7.346 26.457 1 24.69 ? SD SAM 402 B 1 
HETATM 9 C CE SAM . . . C 3 -7.237 -8.937 26.349 1 20.29 ? CE SAM 402 B 1 
HETATM 10 C C5' SAM . . . C 3 -8.805 -7.579 28.141 1 24.63 ? C5' SAM 402 B 1 
HETATM 11 C C4' SAM . . . C 3 -9.42 -6.278 28.631 1 26.66 ? C4' SAM 402 B 1 
HETATM 12 O O4' SAM . . . C 3 -10.803 -6.211 28.256 1 26.06 ? O4' SAM 402 B 1 
HETATM 13 C C3' SAM . . . C 3 -9.381 -6.089 30.133 1 28.42 ? C3' SAM 402 B 1 
HETATM 14 O O3' SAM . . . C 3 -8.264 -5.294 30.525 1 31.43 ? O3' SAM 402 B 1 
HETATM 15 C C2' SAM . . . C 3 -10.664 -5.344 30.414 1 25.29 ? C2' SAM 402 B 1 
HETATM 16 O O2' SAM . . . C 3 -10.575 -3.968 29.997 1 26.31 ? O2' SAM 402 B 1 
HETATM 17 C C1' SAM . . . C 3 -11.598 -5.956 29.412 1 23.29 ? C1' SAM 402 B 1 
HETATM 18 N N9 SAM . . . C 3 -12.289 -7.18 29.815 1 21.48 ? N9 SAM 402 B 1 
HETATM 19 C C8 SAM . . . C 3 -12.493 -8.248 28.991 1 17.94 ? C8 SAM 402 B 1 
HETATM 20 N N7 SAM . . . C 3 -13.236 -9.176 29.551 1 18.65 ? N7 SAM 402 B 1 
HETATM 21 C C5 SAM . . . C 3 -13.526 -8.686 30.791 1 19.51 ? C5 SAM 402 B 1 
HETATM 22 C C6 SAM . . . C 3 -14.31 -9.216 31.804 1 16.27 ? C6 SAM 402 B 1 
HETATM 23 N N6 SAM . . . C 3 -14.946 -10.436 31.647 1 20.37 ? N6 SAM 402 B 1 
HETATM 24 N N1 SAM . . . C 3 -14.408 -8.515 32.937 1 17.38 ? N1 SAM 402 B 1 
HETATM 25 C C2 SAM . . . C 3 -13.789 -7.327 33.004 1 22.49 ? C2 SAM 402 B 1 
HETATM 26 N N3 SAM . . . C 3 -13.029 -6.701 32.085 1 22.27 ? N3 SAM 402 B 1 
HETATM 27 C C4 SAM . . . C 3 -12.944 -7.447 30.981 1 20.08 ? C4 SAM 402 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           227 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#