data_5KJN
#
_model_server_result.job_id            jV2RyBYbxvTmwVLOPufs7A 
_model_server_result.datetime_utc      '2024-11-22 02:56:58' 
_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          5kjn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    5KJN 
#
_exptl.entry_id    5KJN 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            5KJN 
_cell.length_a            154.871 
_cell.length_b            154.871 
_cell.length_c            52.286 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KJN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 4' 
#
_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,F,G,H,I,J,K,L,M,N,O 
_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
metalc ? metalc1 A SG CYS 48 A CYS 52 1_555 L ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc2 A SG CYS 51 A CYS 55 1_555 L ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc3 A SG CYS 61 A CYS 65 1_555 M ZN ZN . A ZN 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc4 A SG CYS 64 A CYS 68 1_555 M ZN ZN . A ZN 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc5 A SG CYS 70 A CYS 74 1_555 L ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? 
metalc ? metalc6 A SG CYS 74 A CYS 78 1_555 L ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc7 A NE2 HIS 82 A HIS 86 1_555 M ZN ZN . A ZN 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc8 A SG CYS 86 A CYS 90 1_555 M ZN ZN . A ZN 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc9 A OE1 GLU 186 A GLU 190 1_555 I NA NA . A NA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? 
metalc ? metalc10 A OE2 GLU 186 A GLU 190 1_555 I NA NA . A NA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.1 ? 
metalc ? metalc11 A SG CYS 205 A CYS 209 1_555 N ZN ZN . A ZN 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc12 A OD1 ASP 238 A ASP 242 1_555 J NA NA . A NA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
metalc ? metalc13 A SG CYS 258 A CYS 262 1_555 N ZN ZN . A ZN 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc14 A SG CYS 260 A CYS 264 1_555 N ZN ZN . A ZN 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc15 A SG CYS 263 A CYS 267 1_555 N ZN ZN . A ZN 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
#
_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 377 n n 
N HN1 SAM sing 378 n n 
N HN2 SAM sing 379 n n 
CA C SAM sing 380 n n 
CA CB SAM sing 381 n n 
CA HA SAM sing 382 n n 
C O SAM doub 383 n n 
C OXT SAM sing 384 n n 
CB CG SAM sing 385 n n 
CB HB1 SAM sing 386 n n 
CB HB2 SAM sing 387 n n 
CG SD SAM sing 388 n n 
CG HG1 SAM sing 389 n n 
CG HG2 SAM sing 390 n n 
SD CE SAM sing 391 n n 
SD C5' SAM sing 392 n n 
CE HE1 SAM sing 393 n n 
CE HE2 SAM sing 394 n n 
CE HE3 SAM sing 395 n n 
C5' C4' SAM sing 396 n n 
C5' "H5'1" SAM sing 397 n n 
C5' "H5'2" SAM sing 398 n n 
C4' O4' SAM sing 399 n n 
C4' C3' SAM sing 400 n n 
C4' H4' SAM sing 401 n n 
O4' C1' SAM sing 402 n n 
C3' O3' SAM sing 403 n n 
C3' C2' SAM sing 404 n n 
C3' H3' SAM sing 405 n n 
O3' HO3' SAM sing 406 n n 
C2' O2' SAM sing 407 n n 
C2' C1' SAM sing 408 n n 
C2' H2' SAM sing 409 n n 
O2' HO2' SAM sing 410 n n 
C1' N9 SAM sing 411 n n 
C1' H1' SAM sing 412 n n 
N9 C8 SAM sing 413 n y 
N9 C4 SAM sing 414 n y 
C8 N7 SAM doub 415 n y 
C8 H8 SAM sing 416 n n 
N7 C5 SAM sing 417 n y 
C5 C6 SAM sing 418 n y 
C5 C4 SAM doub 419 n y 
C6 N6 SAM sing 420 n n 
C6 N1 SAM doub 421 n y 
N6 HN61 SAM sing 422 n n 
N6 HN62 SAM sing 423 n n 
N1 C2 SAM sing 424 n y 
C2 N3 SAM doub 425 n y 
C2 H2 SAM sing 426 n n 
N3 C4 SAM sing 427 n y 
#
_atom_sites.entry_id                     5KJN 
_atom_sites.fract_transf_matrix[1][1]    0.006457 
_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]    0.006457 
_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]    0.019126 
_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 1 501 1000 SAM SAM . 
C 3 BU3 A 1 502 1 BU3 BU3 . 
D 3 BU3 A 1 503 2 BU3 BU3 . 
E 3 BU3 A 1 504 3 BU3 BU3 . 
F 3 BU3 A 1 505 4 BU3 BU3 . 
G 3 BU3 A 1 506 5 BU3 BU3 . 
H 3 BU3 A 1 507 6 BU3 BU3 . 
I 4 NA A 1 508 1 NA NA . 
J 4 NA A 1 509 2 NA NA . 
K 5 6TL A 1 510 1 6TL INH . 
L 6 ZN A 1 511 1 ZN ZN . 
M 6 ZN A 1 512 2 ZN ZN . 
N 6 ZN A 1 513 3 ZN ZN . 
O 7 HOH A 1 601 75 HOH HOH . 
O 7 HOH A 2 602 6 HOH HOH . 
O 7 HOH A 3 603 62 HOH HOH . 
O 7 HOH A 4 604 51 HOH HOH . 
O 7 HOH A 5 605 77 HOH HOH . 
O 7 HOH A 6 606 1 HOH HOH . 
O 7 HOH A 7 607 53 HOH HOH . 
O 7 HOH A 8 608 71 HOH HOH . 
O 7 HOH A 9 609 81 HOH HOH . 
O 7 HOH A 10 610 41 HOH HOH . 
O 7 HOH A 11 611 78 HOH HOH . 
O 7 HOH A 12 612 54 HOH HOH . 
O 7 HOH A 13 613 43 HOH HOH . 
O 7 HOH A 14 614 45 HOH HOH . 
O 7 HOH A 15 615 79 HOH HOH . 
O 7 HOH A 16 616 4 HOH HOH . 
O 7 HOH A 17 617 14 HOH HOH . 
O 7 HOH A 18 618 3 HOH HOH . 
O 7 HOH A 19 619 36 HOH HOH . 
O 7 HOH A 20 620 12 HOH HOH . 
O 7 HOH A 21 621 76 HOH HOH . 
O 7 HOH A 22 622 26 HOH HOH . 
O 7 HOH A 23 623 61 HOH HOH . 
O 7 HOH A 24 624 21 HOH HOH . 
O 7 HOH A 25 625 8 HOH HOH . 
O 7 HOH A 26 626 52 HOH HOH . 
O 7 HOH A 27 627 16 HOH HOH . 
O 7 HOH A 28 628 7 HOH HOH . 
O 7 HOH A 29 629 25 HOH HOH . 
O 7 HOH A 30 630 31 HOH HOH . 
O 7 HOH A 31 631 39 HOH HOH . 
O 7 HOH A 32 632 11 HOH HOH . 
O 7 HOH A 33 633 28 HOH HOH . 
O 7 HOH A 34 634 24 HOH HOH . 
O 7 HOH A 35 635 29 HOH HOH . 
O 7 HOH A 36 636 80 HOH HOH . 
O 7 HOH A 37 637 20 HOH HOH . 
O 7 HOH A 38 638 34 HOH HOH . 
O 7 HOH A 39 639 10 HOH HOH . 
O 7 HOH A 40 640 49 HOH HOH . 
O 7 HOH A 41 641 40 HOH HOH . 
O 7 HOH A 42 642 15 HOH HOH . 
O 7 HOH A 43 643 60 HOH HOH . 
O 7 HOH A 44 644 9 HOH HOH . 
O 7 HOH A 45 645 58 HOH HOH . 
O 7 HOH A 46 646 73 HOH HOH . 
O 7 HOH A 47 647 38 HOH HOH . 
O 7 HOH A 48 648 56 HOH HOH . 
O 7 HOH A 49 649 19 HOH HOH . 
O 7 HOH A 50 650 2 HOH HOH . 
O 7 HOH A 51 651 32 HOH HOH . 
O 7 HOH A 52 652 70 HOH HOH . 
O 7 HOH A 53 653 46 HOH HOH . 
O 7 HOH A 54 654 33 HOH HOH . 
O 7 HOH A 55 655 17 HOH HOH . 
O 7 HOH A 56 656 35 HOH HOH . 
O 7 HOH A 57 657 50 HOH HOH . 
O 7 HOH A 58 658 23 HOH HOH . 
O 7 HOH A 59 659 59 HOH HOH . 
O 7 HOH A 60 660 13 HOH HOH . 
O 7 HOH A 61 661 48 HOH HOH . 
O 7 HOH A 62 662 69 HOH HOH . 
O 7 HOH A 63 663 22 HOH HOH . 
O 7 HOH A 64 664 55 HOH HOH . 
O 7 HOH A 65 665 66 HOH HOH . 
O 7 HOH A 66 666 72 HOH HOH . 
O 7 HOH A 67 667 47 HOH HOH . 
O 7 HOH A 68 668 5 HOH HOH . 
O 7 HOH A 69 669 44 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 -57.996 -15.559 -41.804 1 58.36 ? N SAM 501 A 1 
HETATM 2 C CA SAM . . . B 2 -57.818 -14.413 -40.887 1 56.33 ? CA SAM 501 A 1 
HETATM 3 C C SAM . . . B 2 -58.398 -13.073 -41.473 1 57.68 ? C SAM 501 A 1 
HETATM 4 O O SAM . . . B 2 -58.661 -13.057 -42.69 1 58.14 ? O SAM 501 A 1 
HETATM 5 O OXT SAM . . . B 2 -58.57 -12.118 -40.684 1 58.61 ? OXT SAM 501 A 1 
HETATM 6 C CB SAM . . . B 2 -56.346 -14.266 -40.459 1 52.12 ? CB SAM 501 A 1 
HETATM 7 C CG SAM . . . B 2 -56.114 -15.116 -39.217 1 52.51 ? CG SAM 501 A 1 
HETATM 8 S SD SAM . . . B 2 -57.017 -14.468 -37.79 1 52.12 ? SD SAM 501 A 1 
HETATM 9 C CE SAM . . . B 2 -55.833 -14.125 -36.581 1 49.07 ? CE SAM 501 A 1 
HETATM 10 C C5' SAM . . . B 2 -57.805 -15.957 -37.111 1 51.5 ? C5' SAM 501 A 1 
HETATM 11 C C4' SAM . . . B 2 -59.082 -16.38 -37.814 1 50.45 ? C4' SAM 501 A 1 
HETATM 12 O O4' SAM . . . B 2 -58.784 -16.961 -39.106 1 51.41 ? O4' SAM 501 A 1 
HETATM 13 C C3' SAM . . . B 2 -59.871 -17.452 -37.09 1 49.25 ? C3' SAM 501 A 1 
HETATM 14 O O3' SAM . . . B 2 -60.631 -16.896 -36.026 1 52.46 ? O3' SAM 501 A 1 
HETATM 15 C C2' SAM . . . B 2 -60.678 -18.077 -38.228 1 46.75 ? C2' SAM 501 A 1 
HETATM 16 O O2' SAM . . . B 2 -61.829 -17.314 -38.551 1 45.57 ? O2' SAM 501 A 1 
HETATM 17 C C1' SAM . . . B 2 -59.663 -18.039 -39.379 1 47.1 ? C1' SAM 501 A 1 
HETATM 18 N N9 SAM . . . B 2 -58.86 -19.257 -39.532 1 41.36 ? N9 SAM 501 A 1 
HETATM 19 C C8 SAM . . . B 2 -57.56 -19.442 -39.135 1 39.43 ? C8 SAM 501 A 1 
HETATM 20 N N7 SAM . . . B 2 -57.071 -20.623 -39.429 1 38.89 ? N7 SAM 501 A 1 
HETATM 21 C C5 SAM . . . B 2 -58.128 -21.271 -40.049 1 37.11 ? C5 SAM 501 A 1 
HETATM 22 C C6 SAM . . . B 2 -58.274 -22.58 -40.553 1 35.85 ? C6 SAM 501 A 1 
HETATM 23 N N6 SAM . . . B 2 -57.315 -23.504 -40.494 1 35.77 ? N6 SAM 501 A 1 
HETATM 24 N N1 SAM . . . B 2 -59.48 -22.931 -41.059 1 38.87 ? N1 SAM 501 A 1 
HETATM 25 C C2 SAM . . . B 2 -60.476 -22.03 -41.039 1 41.64 ? C2 SAM 501 A 1 
HETATM 26 N N3 SAM . . . B 2 -60.461 -20.77 -40.581 1 39.7 ? N3 SAM 501 A 1 
HETATM 27 C C4 SAM . . . B 2 -59.244 -20.445 -40.108 1 38.75 ? C4 SAM 501 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           260 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#