data_5BYN # _model_server_result.job_id bzDboryJidCKFkb4dOx6SA _model_server_result.datetime_utc '2025-01-10 22:00:57' _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":"I","auth_seq_id":301}' # _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 . . . I 7 57.037 -0.824 42.815 1 38 ? N 4WM 301 B 1 HETATM 2 O O4 4WM . . . I 7 58.659 0.309 41.502 1 38 ? O4 4WM 301 B 1 HETATM 3 C C12 4WM . . . I 7 58.477 -0.66 42.541 1 38.29 ? C12 4WM 301 B 1 HETATM 4 O O3 4WM . . . I 7 59.141 -0.221 43.725 1 39.46 ? O3 4WM 301 B 1 HETATM 5 C C13 4WM . . . I 7 59.525 -1.292 44.588 1 40.79 ? C13 4WM 301 B 1 HETATM 6 C C16 4WM . . . I 7 59.438 -2.611 43.831 1 41.02 ? C16 4WM 301 B 1 HETATM 7 C C15 4WM . . . I 7 60.955 -1.05 45.052 1 41.76 ? C15 4WM 301 B 1 HETATM 8 C C14 4WM . . . I 7 58.593 -1.318 45.796 1 41.13 ? C14 4WM 301 B 1 HETATM 9 C C8 4WM . . . I 7 56.356 0.476 42.666 1 35.83 ? C8 4WM 301 B 1 HETATM 10 C C9 4WM . . . I 7 55.122 0.51 43.56 1 36.61 ? C9 4WM 301 B 1 HETATM 11 C C10 4WM . . . I 7 55.398 -0.167 44.897 1 37.57 ? C10 4WM 301 B 1 HETATM 12 C C11 4WM . . . I 7 54.715 -1.527 44.972 1 38.11 ? C11 4WM 301 B 1 HETATM 13 O O2 4WM . . . I 7 55.218 -2.252 46.099 1 35.13 ? O2 4WM 301 B 1 HETATM 14 O O1 4WM . . . I 7 53.302 -1.345 45.113 1 40.99 ? O1 4WM 301 B 1 HETATM 15 C C7 4WM . . . I 7 55.937 0.667 41.213 1 34.83 ? C7 4WM 301 B 1 HETATM 16 SE SE 4WM . . . I 7 56.268 -0.807 40.307 1 38.75 ? SE 4WM 301 B 1 HETATM 17 C C2 4WM . . . I 7 54.708 -1.523 39.897 1 36.25 ? C2 4WM 301 B 1 HETATM 18 C C3 4WM . . . I 7 53.644 -1.012 40.861 1 35.94 ? C3 4WM 301 B 1 HETATM 19 C C4 4WM . . . I 7 52.29 -1.645 40.565 1 35.84 ? C4 4WM 301 B 1 HETATM 20 C C5 4WM . . . I 7 52.372 -3.166 40.628 1 37.32 ? C5 4WM 301 B 1 HETATM 21 C C6 4WM . . . I 7 53.458 -3.693 39.698 1 37.65 ? C6 4WM 301 B 1 HETATM 22 C C1 4WM . . . I 7 54.801 -3.041 40.002 1 37.13 ? C1 4WM 301 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #