data_5WBV
#
_model_server_result.job_id            ibIDKPU-SGq3XhuPVcpvEg 
_model_server_result.datetime_utc      '2025-07-03 22:42:45' 
_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          5wbv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    5WBV 
#
_exptl.entry_id    5WBV 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         101.26 
_cell.angle_beta          107.51 
_cell.angle_gamma         89.67 
_cell.entry_id            5WBV 
_cell.length_a            46.324 
_cell.length_b            50.559 
_cell.length_c            74.818 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5WBV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,K,U 1 1 
B,L,M,N,O,P,Q,R,S,T,V 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 M N 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 213 A CYS 275 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc2 A SG CYS 257 A CYS 319 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc3 A SG CYS 259 A CYS 321 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc4 A SG CYS 262 A CYS 324 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc5 B SG CYS 213 B CYS 275 1_555 L ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc6 B SG CYS 257 B CYS 319 1_555 L ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc7 B SG CYS 259 B CYS 321 1_555 L ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc8 B SG CYS 262 B CYS 324 1_555 L ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? 
#
_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                     5WBV 
_atom_sites.fract_transf_matrix[1][1]    0.021587 
_atom_sites.fract_transf_matrix[1][2]    -0.000124 
_atom_sites.fract_transf_matrix[1][3]    0.006929 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019779 
_atom_sites.fract_transf_matrix[2][3]    0.004099 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.014313 
_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 2 ZN A 1 401 400 ZN ZN . 
D 3 SAM A 1 402 500 SAM SAM . 
E 4 9ZY A 1 403 600 9ZY XXX . 
F 5 UNX A 1 404 33 UNX UNX . 
G 5 UNX A 1 405 34 UNX UNX . 
H 5 UNX A 1 406 36 UNX UNX . 
I 5 UNX A 1 407 37 UNX UNX . 
J 5 UNX A 1 408 41 UNX UNX . 
K 5 UNX A 1 409 42 UNX UNX . 
L 2 ZN B 1 401 400 ZN ZN . 
M 3 SAM B 1 402 500 SAM SAM . 
N 4 9ZY B 1 403 600 9ZY XXX . 
O 5 UNX B 1 404 32 UNX UNX . 
P 5 UNX B 1 405 38 UNX UNX . 
Q 5 UNX B 1 406 39 UNX UNX . 
R 5 UNX B 1 407 40 UNX UNX . 
S 5 UNX B 1 408 43 UNX UNX . 
T 5 UNX B 1 409 44 UNX UNX . 
U 6 HOH A 1 501 20 HOH HOH . 
U 6 HOH A 2 502 1 HOH HOH . 
U 6 HOH A 3 503 24 HOH HOH . 
U 6 HOH A 4 504 13 HOH HOH . 
U 6 HOH A 5 505 25 HOH HOH . 
U 6 HOH A 6 506 2 HOH HOH . 
U 6 HOH A 7 507 26 HOH HOH . 
U 6 HOH A 8 508 9 HOH HOH . 
U 6 HOH A 9 509 21 HOH HOH . 
U 6 HOH A 10 510 17 HOH HOH . 
U 6 HOH A 11 511 27 HOH HOH . 
U 6 HOH A 12 512 6 HOH HOH . 
U 6 HOH A 13 513 28 HOH HOH . 
U 6 HOH A 14 514 22 HOH HOH . 
U 6 HOH A 15 515 11 HOH HOH . 
U 6 HOH A 16 516 14 HOH HOH . 
U 6 HOH A 17 517 4 HOH HOH . 
U 6 HOH A 18 518 31 HOH HOH . 
U 6 HOH A 19 519 10 HOH HOH . 
U 6 HOH A 20 520 29 HOH HOH . 
V 6 HOH B 1 501 3 HOH HOH . 
V 6 HOH B 2 502 5 HOH HOH . 
V 6 HOH B 3 503 16 HOH HOH . 
V 6 HOH B 4 504 7 HOH HOH . 
V 6 HOH B 5 505 30 HOH HOH . 
V 6 HOH B 6 506 8 HOH HOH . 
V 6 HOH B 7 507 15 HOH HOH . 
V 6 HOH B 8 508 12 HOH HOH . 
V 6 HOH B 9 509 19 HOH HOH . 
V 6 HOH B 10 510 23 HOH HOH . 
V 6 HOH B 11 511 18 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 . . . D 3 13.009 49.521 5.912 1 51.98 ? N SAM 402 A 1 
HETATM 2 C CA SAM . . . D 3 11.659 49.241 5.402 1 48.38 ? CA SAM 402 A 1 
HETATM 3 C C SAM . . . D 3 10.627 50.12 6.138 1 47.71 ? C SAM 402 A 1 
HETATM 4 O O SAM . . . D 3 9.593 50.431 5.503 1 46.84 ? O SAM 402 A 1 
HETATM 5 O OXT SAM . . . D 3 10.924 50.502 7.286 1 45.8 ? OXT SAM 402 A 1 
HETATM 6 C CB SAM . . . D 3 11.215 47.777 5.558 1 46.67 ? CB SAM 402 A 1 
HETATM 7 C CG SAM . . . D 3 11.317 46.987 4.207 1 47.77 ? CG SAM 402 A 1 
HETATM 8 S SD SAM . . . D 3 10.091 47.493 2.982 1 44.9 ? SD SAM 402 A 1 
HETATM 9 C CE SAM . . . D 3 9.401 45.921 2.634 1 43.3 ? CE SAM 402 A 1 
HETATM 10 C C5' SAM . . . D 3 11.116 47.797 1.526 1 44.67 ? C5' SAM 402 A 1 
HETATM 11 C C4' SAM . . . D 3 11.771 49.193 1.477 1 46.59 ? C4' SAM 402 A 1 
HETATM 12 O O4' SAM . . . D 3 12.89 49.202 2.394 1 47.94 ? O4' SAM 402 A 1 
HETATM 13 C C3' SAM . . . D 3 12.356 49.653 0.14 1 48.72 ? C3' SAM 402 A 1 
HETATM 14 O O3' SAM . . . D 3 11.42 50.333 -0.693 1 52.91 ? O3' SAM 402 A 1 
HETATM 15 C C2' SAM . . . D 3 13.474 50.587 0.594 1 50.29 ? C2' SAM 402 A 1 
HETATM 16 O O2' SAM . . . D 3 12.969 51.829 1.083 1 49.39 ? O2' SAM 402 A 1 
HETATM 17 C C1' SAM . . . D 3 14.022 49.797 1.779 1 49.1 ? C1' SAM 402 A 1 
HETATM 18 N N9 SAM . . . D 3 14.985 48.745 1.441 1 46.25 ? N9 SAM 402 A 1 
HETATM 19 C C8 SAM . . . D 3 15.069 47.508 2.026 1 45.42 ? C8 SAM 402 A 1 
HETATM 20 N N7 SAM . . . D 3 16.034 46.756 1.557 1 45.39 ? N7 SAM 402 A 1 
HETATM 21 C C5 SAM . . . D 3 16.636 47.556 0.593 1 44.39 ? C5 SAM 402 A 1 
HETATM 22 C C6 SAM . . . D 3 17.771 47.367 -0.23 1 40.05 ? C6 SAM 402 A 1 
HETATM 23 N N6 SAM . . . D 3 18.599 46.315 -0.128 1 39.05 ? N6 SAM 402 A 1 
HETATM 24 N N1 SAM . . . D 3 18.108 48.37 -1.076 1 37.05 ? N1 SAM 402 A 1 
HETATM 25 C C2 SAM . . . D 3 17.41 49.509 -1.043 1 36.88 ? C2 SAM 402 A 1 
HETATM 26 N N3 SAM . . . D 3 16.353 49.817 -0.286 1 42.24 ? N3 SAM 402 A 1 
HETATM 27 C C4 SAM . . . D 3 16 48.784 0.508 1 45.58 ? C4 SAM 402 A 1 
#
_model_server_stats.io_time_ms              76 
_model_server_stats.parse_time_ms           116 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#