data_7NEE # _model_server_result.job_id F2_NwpVIqW0Z2x1jUlYUkg _model_server_result.datetime_utc '2025-08-31 09:35:01' _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 7nee # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7NEE # _exptl.entry_id 7NEE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 342.37 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,3S)-3-(4-ammoniobutyl)-1-benzyl-1,4-azaphosphinan-1-ium-3-carboxylate 4,4-dioxide' _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 7NEE _cell.length_a 64.17 _cell.length_b 95.5 _cell.length_c 157.22 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NEE _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 disulf ? disulf1 A SG CYS 155 A CYS 178 1_555 A SG CYS 168 A CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf2 A SG CYS 227 A CYS 250 1_555 A SG CYS 251 A CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? disulf ? disulf3 A SG CYS 242 A CYS 265 1_555 A SG CYS 256 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc1 A ND1 HIS 158 A HIS 181 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.686 ? metalc ? metalc2 A OE1 GLU 161 A GLU 184 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc3 A ND1 HIS 287 A HIS 310 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc4 B O4 U9B . A U9B 501 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.827 ? # _chem_comp.formula 'C16 H27 N2 O4 P 2' _chem_comp.formula_weight 342.37 _chem_comp.id U9B _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,3S)-3-(4-ammoniobutyl)-1-benzyl-1,4-azaphosphinan-1-ium-3-carboxylate 4,4-dioxide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 4-[(1~{R},3~{S})-3-carboxy-4-oxidanyl-4-oxidanylidene-1-(phenylmethyl)-1,4$l^{5}-azaphosphinan-1-ium-3-yl]butylazanium # 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 C16 C15 U9B sing 358 n n C16 P1 U9B sing 359 n n C15 N2 U9B sing 360 n n O4 P1 U9B doub 361 n n N2 C8 U9B sing 362 n n N2 C7 U9B sing 363 n n C8 C9 U9B sing 364 n n P1 O3 U9B sing 365 n n P1 C5 U9B sing 366 n n C7 C5 U9B sing 367 n n C9 C14 U9B doub 368 n y C9 C10 U9B sing 369 n y C5 C4 U9B sing 370 n n C5 C6 U9B sing 371 n n C14 C13 U9B sing 372 n y C4 C3 U9B sing 373 n n C10 C11 U9B doub 374 n y C6 O2 U9B doub 375 n n C6 O1 U9B sing 376 n n C13 C12 U9B doub 377 n y C3 C2 U9B sing 378 n n C2 C1 U9B sing 379 n n C11 C12 U9B sing 380 n y C1 N1 U9B sing 381 n n C1 H5 U9B sing 382 n n C1 H4 U9B sing 383 n n C2 H7 U9B sing 384 n n C2 H6 U9B sing 385 n n C7 H12 U9B sing 386 n n C7 H13 U9B sing 387 n n C8 H15 U9B sing 388 n n C8 H16 U9B sing 389 n n C15 H23 U9B sing 390 n n C15 H22 U9B sing 391 n n C16 H24 U9B sing 392 n n C16 H25 U9B sing 393 n n N1 H3 U9B sing 394 n n N1 H1 U9B sing 395 n n N1 H2 U9B sing 396 n n C3 H9 U9B sing 397 n n C3 H8 U9B sing 398 n n C4 H11 U9B sing 399 n n C4 H10 U9B sing 400 n n O1 H26 U9B sing 401 n n N2 H14 U9B sing 402 n n C10 H17 U9B sing 403 n n C11 H18 U9B sing 404 n n C12 H19 U9B sing 405 n n C13 H20 U9B sing 406 n n C14 H21 U9B sing 407 n n O3 H27 U9B sing 408 n n # _atom_sites.entry_id 7NEE _atom_sites.fract_transf_matrix[1][1] 0.015584 _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] 0.010471 _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] 0.006361 _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 U9B A 1 501 501 U9B 580 . C 3 ZN A 1 502 1 ZN ZN . D 4 HOH A 1 601 3 HOH HOH . D 4 HOH A 2 602 18 HOH HOH . D 4 HOH A 3 603 19 HOH HOH . D 4 HOH A 4 604 11 HOH HOH . D 4 HOH A 5 605 7 HOH HOH . D 4 HOH A 6 606 4 HOH HOH . D 4 HOH A 7 607 16 HOH HOH . D 4 HOH A 8 608 13 HOH HOH . D 4 HOH A 9 609 12 HOH HOH . D 4 HOH A 10 610 6 HOH HOH . D 4 HOH A 11 611 17 HOH HOH . D 4 HOH A 12 612 2 HOH HOH . D 4 HOH A 13 613 14 HOH HOH . D 4 HOH A 14 614 9 HOH HOH . D 4 HOH A 15 615 8 HOH HOH . D 4 HOH A 16 616 5 HOH HOH . D 4 HOH A 17 617 21 HOH HOH . D 4 HOH A 18 618 20 HOH HOH . D 4 HOH A 19 619 10 HOH HOH . D 4 HOH A 20 620 1 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 C C1 U9B . . . B 2 8.161 13.522 25.952 1 47.87 0 C1 U9B 501 A 1 HETATM 2 C C2 U9B . . . B 2 8.931 13.514 24.646 1 46.44 0 C2 U9B 501 A 1 HETATM 3 C C5 U9B . . . B 2 11.764 15.581 22.94 1 44.41 0 C5 U9B 501 A 1 HETATM 4 C C6 U9B . . . B 2 12.361 16.181 24.234 1 45.27 0 C6 U9B 501 A 1 HETATM 5 C C7 U9B . . . B 2 12.579 14.289 22.779 1 46.06 0 C7 U9B 501 A 1 HETATM 6 C C8 U9B . . . B 2 12.523 12.091 21.551 1 54.86 0 C8 U9B 501 A 1 HETATM 7 C C15 U9B . . . B 2 12.984 14.268 20.378 1 48.18 0 C15 U9B 501 A 1 HETATM 8 C C16 U9B . . . B 2 12.499 15.718 20.187 1 46.34 0 C16 U9B 501 A 1 HETATM 9 N N1 U9B . . . B 2 7.287 14.711 26.088 1 48.32 1 N1 U9B 501 A 1 HETATM 10 C C3 U9B . . . B 2 9.994 14.601 24.642 1 45.62 0 C3 U9B 501 A 1 HETATM 11 C C4 U9B . . . B 2 10.277 15.223 23.274 1 45.33 0 C4 U9B 501 A 1 HETATM 12 O O1 U9B . . . B 2 11.751 17.105 24.765 1 44.2 0 O1 U9B 501 A 1 HETATM 13 O O2 U9B . . . B 2 13.436 15.741 24.713 1 47.35 -1 O2 U9B 501 A 1 HETATM 14 N N2 U9B . . . B 2 12.259 13.586 21.501 1 49.84 1 N2 U9B 501 A 1 HETATM 15 C C9 U9B . . . B 2 12.193 11.475 22.888 1 60.03 0 C9 U9B 501 A 1 HETATM 16 C C10 U9B . . . B 2 13.196 11.239 23.825 1 63.43 0 C10 U9B 501 A 1 HETATM 17 C C11 U9B . . . B 2 12.891 10.719 25.076 1 64.78 0 C11 U9B 501 A 1 HETATM 18 C C12 U9B . . . B 2 11.572 10.445 25.404 1 66.84 0 C12 U9B 501 A 1 HETATM 19 C C13 U9B . . . B 2 10.567 10.688 24.491 1 62.81 0 C13 U9B 501 A 1 HETATM 20 C C14 U9B . . . B 2 10.876 11.206 23.239 1 62.83 0 C14 U9B 501 A 1 HETATM 21 P P1 U9B . . . B 2 11.984 16.779 21.579 1 41.32 0 P1 U9B 501 A 1 HETATM 22 O O3 U9B . . . B 2 13.178 17.526 21.971 1 42.11 0 O3 U9B 501 A 1 HETATM 23 O O4 U9B . . . B 2 10.891 17.609 21.1 1 36.87 -1 O4 U9B 501 A 1 HETATM 24 H H5 U9B . . . B 2 8.79 13.506 26.699 1 47.71 0 H5 U9B 501 A 1 HETATM 25 H H4 U9B . . . B 2 7.609 12.72 26.006 1 47.77 0 H4 U9B 501 A 1 HETATM 26 H H7 U9B . . . B 2 9.358 12.647 24.526 1 46.79 0 H7 U9B 501 A 1 HETATM 27 H H6 U9B . . . B 2 8.312 13.664 23.901 1 46.53 0 H6 U9B 501 A 1 HETATM 28 H H12 U9B . . . B 2 13.534 14.511 22.792 1 46.56 0 H12 U9B 501 A 1 HETATM 29 H H13 U9B . . . B 2 12.389 13.701 23.536 1 46.67 0 H13 U9B 501 A 1 HETATM 30 H H15 U9B . . . B 2 13.473 11.929 21.349 1 54.83 0 H15 U9B 501 A 1 HETATM 31 H H16 U9B . . . B 2 11.985 11.65 20.854 1 54.8 0 H16 U9B 501 A 1 HETATM 32 H H23 U9B . . . B 2 13.941 14.269 20.565 1 48.17 0 H23 U9B 501 A 1 HETATM 33 H H22 U9B . . . B 2 12.836 13.769 19.554 1 48.17 0 H22 U9B 501 A 1 HETATM 34 H H24 U9B . . . B 2 11.74 15.698 19.563 1 45.42 0 H24 U9B 501 A 1 HETATM 35 H H25 U9B . . . B 2 13.217 16.209 19.728 1 45.44 0 H25 U9B 501 A 1 HETATM 36 H H3 U9B . . . B 2 7.783 15.469 26.076 1 47.99 0 H3 U9B 501 A 1 HETATM 37 H H1 U9B . . . B 2 6.836 14.669 26.874 1 48.17 0 H1 U9B 501 A 1 HETATM 38 H H2 U9B . . . B 2 6.69 14.733 25.405 1 48.08 0 H2 U9B 501 A 1 HETATM 39 H H9 U9B . . . B 2 9.719 15.313 25.256 1 45.69 0 H9 U9B 501 A 1 HETATM 40 H H8 U9B . . . B 2 10.824 14.217 24.994 1 45.81 0 H8 U9B 501 A 1 HETATM 41 H H11 U9B . . . B 2 9.955 14.608 22.586 1 45.23 0 H11 U9B 501 A 1 HETATM 42 H H10 U9B . . . B 2 9.751 16.046 23.198 1 45.05 0 H10 U9B 501 A 1 HETATM 43 H H14 U9B . . . B 2 11.368 13.669 21.343 1 49.56 0 H14 U9B 501 A 1 HETATM 44 H H17 U9B . . . B 2 14.093 11.435 23.608 1 62.87 0 H17 U9B 501 A 1 HETATM 45 H H18 U9B . . . B 2 13.58 10.549 25.699 1 64.79 0 H18 U9B 501 A 1 HETATM 46 H H19 U9B . . . B 2 11.364 10.078 26.248 1 65.22 0 H19 U9B 501 A 1 HETATM 47 H H20 U9B . . . B 2 9.67 10.489 24.712 1 63.57 0 H20 U9B 501 A 1 HETATM 48 H H21 U9B . . . B 2 10.183 11.378 22.621 1 62.12 0 H21 U9B 501 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 589 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #