data_5BYN
#
_model_server_result.job_id            9ihoZJTZVZeSyLwSYqW35Q 
_model_server_result.datetime_utc      '2025-01-10 22:01:42' 
_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          5byn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":306}' 
#
_entry.id    5BYN 
#
_exptl.entry_id    5BYN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              380.382 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4R)-4-{[(S)-tert-butoxy(hydroxy)methyl]amino}-5-[(1S)-cyclohex-2-en-1-ylselanyl]pentane-1,1-diol 
_entity.pdbx_number_of_molecules    2 
_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            5BYN 
_cell.length_a            190.64 
_cell.length_b            190.64 
_cell.length_c            190.64 
_cell.Z_PDB               96 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5BYN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        196 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'F 2 3' 
#
_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,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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 7 H N N 
? 7 I 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 OE1 GLU 8 A GLU 8 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc2 A OD1 ASP 10 A ASP 10 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc3 A OD2 ASP 10 A ASP 10 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc4 A OD2 ASP 10 A ASP 10 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc5 A O TYR 12 A TYR 12 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? 
metalc ? metalc6 A OD1 ASN 14 A ASN 14 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc7 A OD2 ASP 19 A ASP 19 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc8 A NE2 HIS 24 A HIS 24 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc9 A OE1 GLU 87 A GLU 87 1_555 E CD CD . A CD 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc10 A OE2 GLU 87 A GLU 87 1_555 E CD CD . A CD 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc11 C CA CA . A CA 301 1_555 N O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc12 C CA CA . A CA 301 1_555 N O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? 
metalc ? metalc13 D MN MN . A MN 302 1_555 N O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc14 D MN MN . A MN 302 1_555 N O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? 
metalc ? metalc15 E CD CD . A CD 303 1_555 N O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc16 E CD CD . A CD 303 1_555 N O HOH . A HOH 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc17 B OE1 GLU 8 B GLU 8 1_555 K MN MN . B MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? 
metalc ? metalc18 B OD1 ASP 10 B ASP 10 1_555 J CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc19 B OD2 ASP 10 B ASP 10 1_555 J CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc20 B OD2 ASP 10 B ASP 10 1_555 K MN MN . B MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc21 B O TYR 12 B TYR 12 1_555 J CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc22 B OD2 ASP 19 B ASP 19 1_555 J CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? 
metalc ? metalc23 B OD1 ASP 19 B ASP 19 1_555 K MN MN . B MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc24 B NE2 HIS 24 B HIS 24 1_555 K MN MN . B MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc25 J CA CA . B CA 302 1_555 O O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc26 J CA CA . B CA 302 1_555 O O HOH . B HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc27 K MN MN . B MN 303 1_555 O O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
metalc ? metalc28 K MN MN . B MN 303 1_555 O O HOH . B HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? 
#
_chem_comp.formula           'C16 H31 N O4 Se' 
_chem_comp.formula_weight    380.382 
_chem_comp.id                4WM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4R)-4-{[(S)-tert-butoxy(hydroxy)methyl]amino}-5-[(1S)-cyclohex-2-en-1-ylselanyl]pentane-1,1-diol 
_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
C1 C2 4WM sing 1 n n 
C1 C6 4WM sing 2 n n 
C2 SE 4WM sing 3 n n 
C2 C3 4WM sing 4 n n 
C6 C5 4WM sing 5 n n 
SE C7 4WM sing 6 n n 
C5 C4 4WM sing 7 n n 
C4 C3 4WM doub 8 n n 
C7 C8 4WM sing 9 n n 
O4 C12 4WM sing 10 n n 
C8 N 4WM sing 11 n n 
C8 C9 4WM sing 12 n n 
C12 N 4WM sing 13 n n 
C12 O3 4WM sing 14 n n 
C9 C10 4WM sing 15 n n 
O3 C13 4WM sing 16 n n 
C16 C13 4WM sing 17 n n 
C10 C11 4WM sing 18 n n 
C13 C14 4WM sing 19 n n 
C13 C15 4WM sing 20 n n 
C11 O2 4WM sing 21 n n 
C11 O1 4WM sing 22 n n 
N H1 4WM sing 23 n n 
O4 H3 4WM sing 24 n n 
C12 H4 4WM sing 25 n n 
C16 H5 4WM sing 26 n n 
C16 H6 4WM sing 27 n n 
C16 H7 4WM sing 28 n n 
C15 H8 4WM sing 29 n n 
C15 H9 4WM sing 30 n n 
C15 H10 4WM sing 31 n n 
C14 H11 4WM sing 32 n n 
C14 H12 4WM sing 33 n n 
C14 H13 4WM sing 34 n n 
C8 H14 4WM sing 35 n n 
C9 H15 4WM sing 36 n n 
C9 H16 4WM sing 37 n n 
C10 H17 4WM sing 38 n n 
C10 H18 4WM sing 39 n n 
O2 H19 4WM sing 40 n n 
O1 H20 4WM sing 41 n n 
C7 H21 4WM sing 42 n n 
C7 H22 4WM sing 43 n n 
C2 H23 4WM sing 44 n n 
C3 H24 4WM sing 45 n n 
C4 H26 4WM sing 46 n n 
C5 H28 4WM sing 47 n n 
C5 H29 4WM sing 48 n n 
C6 H30 4WM sing 49 n n 
C6 H31 4WM sing 50 n n 
C1 H32 4WM sing 51 n n 
C1 H33 4WM sing 52 n n 
C11 H2 4WM sing 53 n n 
#
_atom_sites.entry_id                     5BYN 
_atom_sites.fract_transf_matrix[1][1]    0.005245 
_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]    0.005245 
_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]    0.005245 
_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 CA A 1 301 238 CA CA . 
D 3 MN A 1 302 239 MN MN . 
E 4 CD A 1 303 240 CD CD . 
F 5 PEG A 1 304 242 PEG PEG . 
G 6 EDO A 1 305 243 EDO EDO . 
H 7 4WM A 1 306 240 4WM 4WM . 
I 7 4WM B 1 301 241 4WM 4WM . 
J 2 CA B 1 302 238 CA CA . 
K 3 MN B 1 303 239 MN MN . 
L 6 EDO B 1 304 241 EDO EDO . 
M 6 EDO B 1 305 242 EDO EDO . 
N 8 HOH A 1 401 23 HOH HOH . 
N 8 HOH A 2 402 12 HOH HOH . 
N 8 HOH A 3 403 50 HOH HOH . 
N 8 HOH A 4 404 53 HOH HOH . 
N 8 HOH A 5 405 17 HOH HOH . 
N 8 HOH A 6 406 49 HOH HOH . 
N 8 HOH A 7 407 1 HOH HOH . 
N 8 HOH A 8 408 47 HOH HOH . 
N 8 HOH A 9 409 60 HOH HOH . 
N 8 HOH A 10 410 65 HOH HOH . 
N 8 HOH A 11 411 59 HOH HOH . 
N 8 HOH A 12 412 48 HOH HOH . 
N 8 HOH A 13 413 8 HOH HOH . 
N 8 HOH A 14 414 2 HOH HOH . 
N 8 HOH A 15 415 61 HOH HOH . 
N 8 HOH A 16 416 24 HOH HOH . 
N 8 HOH A 17 417 16 HOH HOH . 
N 8 HOH A 18 418 43 HOH HOH . 
N 8 HOH A 19 419 36 HOH HOH . 
N 8 HOH A 20 420 56 HOH HOH . 
N 8 HOH A 21 421 15 HOH HOH . 
N 8 HOH A 22 422 42 HOH HOH . 
N 8 HOH A 23 423 63 HOH HOH . 
N 8 HOH A 24 424 37 HOH HOH . 
N 8 HOH A 25 425 30 HOH HOH . 
N 8 HOH A 26 426 13 HOH HOH . 
N 8 HOH A 27 427 57 HOH HOH . 
N 8 HOH A 28 428 21 HOH HOH . 
N 8 HOH A 29 429 39 HOH HOH . 
N 8 HOH A 30 430 19 HOH HOH . 
N 8 HOH A 31 431 33 HOH HOH . 
N 8 HOH A 32 432 51 HOH HOH . 
O 8 HOH B 1 401 44 HOH HOH . 
O 8 HOH B 2 402 26 HOH HOH . 
O 8 HOH B 3 403 54 HOH HOH . 
O 8 HOH B 4 404 58 HOH HOH . 
O 8 HOH B 5 405 14 HOH HOH . 
O 8 HOH B 6 406 40 HOH HOH . 
O 8 HOH B 7 407 34 HOH HOH . 
O 8 HOH B 8 408 45 HOH HOH . 
O 8 HOH B 9 409 5 HOH HOH . 
O 8 HOH B 10 410 64 HOH HOH . 
O 8 HOH B 11 411 10 HOH HOH . 
O 8 HOH B 12 412 22 HOH HOH . 
O 8 HOH B 13 413 41 HOH HOH . 
O 8 HOH B 14 414 7 HOH HOH . 
O 8 HOH B 15 415 35 HOH HOH . 
O 8 HOH B 16 416 20 HOH HOH . 
O 8 HOH B 17 417 46 HOH HOH . 
O 8 HOH B 18 418 6 HOH HOH . 
O 8 HOH B 19 419 52 HOH HOH . 
O 8 HOH B 20 420 3 HOH HOH . 
O 8 HOH B 21 421 25 HOH HOH . 
O 8 HOH B 22 422 18 HOH HOH . 
O 8 HOH B 23 423 27 HOH HOH . 
O 8 HOH B 24 424 55 HOH HOH . 
O 8 HOH B 25 425 38 HOH HOH . 
O 8 HOH B 26 426 31 HOH HOH . 
O 8 HOH B 27 427 29 HOH HOH . 
O 8 HOH B 28 428 4 HOH HOH . 
O 8 HOH B 29 429 11 HOH HOH . 
O 8 HOH B 30 430 32 HOH HOH . 
O 8 HOH B 31 431 28 HOH HOH . 
O 8 HOH B 32 432 9 HOH HOH . 
O 8 HOH B 33 433 62 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 4WM . . . H 7 47.169 2.228 41.218 1 44.01 ? N 4WM 306 A 1 
HETATM 2 O O4 4WM . . . H 7 47.302 0.086 40.203 1 42.07 ? O4 4WM 306 A 1 
HETATM 3 C C12 4WM . . . H 7 47.806 1.426 40.157 1 42.7 ? C12 4WM 306 A 1 
HETATM 4 O O3 4WM . . . H 7 47.513 2.002 38.883 1 43.83 ? O3 4WM 306 A 1 
HETATM 5 C C13 4WM . . . H 7 48.649 2.608 38.265 1 44.27 ? C13 4WM 306 A 1 
HETATM 6 C C16 4WM . . . H 7 48.853 4.007 38.833 1 42.89 ? C16 4WM 306 A 1 
HETATM 7 C C15 4WM . . . H 7 49.872 1.747 38.551 1 45.2 ? C15 4WM 306 A 1 
HETATM 8 C C14 4WM . . . H 7 48.418 2.684 36.76 1 46.07 ? C14 4WM 306 A 1 
HETATM 9 C C8 4WM . . . H 7 45.888 1.607 41.605 1 44.52 ? C8 4WM 306 A 1 
HETATM 10 C C9 4WM . . . H 7 45.089 2.581 42.463 1 45.87 ? C9 4WM 306 A 1 
HETATM 11 C C10 4WM . . . H 7 43.863 1.903 43.062 1 47.52 ? C10 4WM 306 A 1 
HETATM 12 C C11 4WM . . . H 7 43.38 2.644 44.302 1 48.22 ? C11 4WM 306 A 1 
HETATM 13 O O2 4WM . . . H 7 42.181 2.03 44.789 1 49.87 ? O2 4WM 306 A 1 
HETATM 14 O O1 4WM . . . H 7 44.39 2.589 45.316 1 41.6 ? O1 4WM 306 A 1 
HETATM 15 C C7 4WM . . . H 7 46.158 0.335 42.398 1 43.31 ? C7 4WM 306 A 1 
HETATM 16 SE SE 4WM . . . H 7 46.885 0.751 43.949 1 44.01 ? SE 4WM 306 A 1 
HETATM 17 C C2 4WM . . . H 7 45.728 0.293 45.201 1 42.94 ? C2 4WM 306 A 1 
HETATM 18 C C3 4WM . . . H 7 46.486 -0.26 46.413 1 40.09 ? C3 4WM 306 A 1 
HETATM 19 C C4 4WM . . . H 7 45.712 -1.255 47.282 1 41.07 ? C4 4WM 306 A 1 
HETATM 20 C C5 4WM . . . H 7 44.196 -1.136 47.134 1 44.28 ? C5 4WM 306 A 1 
HETATM 21 C C6 4WM . . . H 7 43.735 -1.219 45.676 1 45.16 ? C6 4WM 306 A 1 
HETATM 22 C C1 4WM . . . H 7 44.761 -0.749 44.642 1 43.33 ? C1 4WM 306 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           348 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           22 
#