data_8HMB # _model_server_result.job_id e9Rmm7p2XFSCn5fia6lRaw _model_server_result.datetime_utc '2024-11-14 17:58:47' _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 8hmb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":2311}' # _entry.id 8HMB # _exptl.entry_id 8HMB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 506.57 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3R)-1-benzylpiperidin-3-yl methyl (2R,3R,4R,5R,6S)-2,6-dimethyl-4-(3-nitrophenyl)piperidine-3,5-dicarboxylate' _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 8HMB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8HMB _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,P,Q,R,S,T,U,V,W,X,Y _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 ? _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 6 _struct_asym.id N _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 B SG CYS 298 D CYS 298 1_555 B SG CYS 326 D CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 316 D CYS 316 1_555 B SG CYS 332 D CYS 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 1058 D CYS 1078 1_555 B SG CYS 1069 D CYS 1089 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 1431 D CYS 1479 1_555 B SG CYS 1447 D CYS 1495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 C SG CYS 303 E CYS 303 1_555 C SG CYS 1044 E CYS 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 354 E CYS 354 1_555 C SG CYS 1059 E CYS 1059 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 C SG CYS 904 E CYS 904 1_555 C SG CYS 974 E CYS 974 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 C ND2 ASN 92 E ASN 92 1_555 R C1 NAG . E NAG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 C ND2 ASN 184 E ASN 184 1_555 S C1 NAG . E NAG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 C ND2 ASN 324 E ASN 324 1_555 T C1 NAG . E NAG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale4 C ND2 ASN 348 E ASN 348 1_555 X C1 NAG . E NAG 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 C ND2 ASN 468 E ASN 468 1_555 V C1 NAG . E NAG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 C ND2 ASN 613 E ASN 613 1_555 W C1 NAG . E NAG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale7 C ND2 ASN 781 E ASN 781 1_555 U C1 NAG . E NAG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 C ND2 ASN 895 E ASN 895 1_555 Y C1 NAG . E NAG 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? metalc ? metalc1 B OE1 GLU 363 D GLU 363 1_555 P CA CA . D CA 2313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc2 B OE2 GLU 363 D GLU 363 1_555 Q CA CA . D CA 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc3 B OE2 GLU 706 D GLU 706 1_555 Q CA CA . D CA 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc4 B OE1 GLU 1115 D GLU 1135 1_555 Q CA CA . D CA 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? # _chem_comp.formula 'C28 H32 N3 O6 1' _chem_comp.formula_weight 506.57 _chem_comp.id A1AC8 _chem_comp.mon_nstd_flag . _chem_comp.name '(3R)-1-benzylpiperidin-3-yl methyl (2R,3R,4R,5R,6S)-2,6-dimethyl-4-(3-nitrophenyl)piperidine-3,5-dicarboxylate' _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 C35 C31 A1AC8 doub 133 n y C35 C32 A1AC8 sing 134 n y C31 C24 A1AC8 sing 135 n y C37 O03 A1AC8 sing 136 n n C32 C25 A1AC8 doub 137 n y C24 C19 A1AC8 doub 138 n y O05 N09 A1AC8 sing 139 n n O06 N09 A1AC8 doub 140 n n C25 C19 A1AC8 sing 141 n y C19 C15 A1AC8 sing 142 n n N09 C33 A1AC8 sing 143 n n O03 C29 A1AC8 sing 144 n n C15 N07 A1AC8 sing 145 n n O04 C29 A1AC8 doub 146 n n C29 C20 A1AC8 sing 147 n n C33 C27 A1AC8 doub 148 n y C33 C36 A1AC8 sing 149 n y N07 C12 A1AC8 sing 150 n n N07 C14 A1AC8 sing 151 n n C27 C22 A1AC8 sing 152 n y C36 C34 A1AC8 doub 153 n y C12 C10 A1AC8 sing 154 n n C14 C13 A1AC8 sing 155 n n C30 C23 A1AC8 sing 156 n n C20 C23 A1AC8 doub 157 n n C20 C16 A1AC8 sing 158 n n C22 C16 A1AC8 sing 159 n n C22 C28 A1AC8 doub 160 n y C34 C28 A1AC8 sing 161 n y C23 N08 A1AC8 sing 162 n n C10 O01 A1AC8 sing 163 n n C10 C11 A1AC8 sing 164 n n C16 C17 A1AC8 sing 165 n n C13 C11 A1AC8 sing 166 n n O01 C18 A1AC8 sing 167 n n N08 C21 A1AC8 sing 168 n n C18 C17 A1AC8 sing 169 n n C18 O02 A1AC8 doub 170 n n C17 C21 A1AC8 doub 171 n n C21 C26 A1AC8 sing 172 n n C10 H1 A1AC8 sing 173 n n C11 H2 A1AC8 sing 174 n n C11 H3 A1AC8 sing 175 n n C12 H4 A1AC8 sing 176 n n C12 H5 A1AC8 sing 177 n n C13 H6 A1AC8 sing 178 n n C13 H7 A1AC8 sing 179 n n C14 H8 A1AC8 sing 180 n n C14 H9 A1AC8 sing 181 n n C15 H10 A1AC8 sing 182 n n C15 H11 A1AC8 sing 183 n n C16 H12 A1AC8 sing 184 n n C24 H17 A1AC8 sing 185 n n C25 H18 A1AC8 sing 186 n n C26 H19 A1AC8 sing 187 n n C26 H20 A1AC8 sing 188 n n C26 H21 A1AC8 sing 189 n n C27 H22 A1AC8 sing 190 n n C28 H23 A1AC8 sing 191 n n C30 H24 A1AC8 sing 192 n n C30 H25 A1AC8 sing 193 n n C30 H26 A1AC8 sing 194 n n C31 H27 A1AC8 sing 195 n n C32 H28 A1AC8 sing 196 n n C34 H29 A1AC8 sing 197 n n C35 H30 A1AC8 sing 198 n n C36 H31 A1AC8 sing 199 n n C37 H32 A1AC8 sing 200 n n C37 H33 A1AC8 sing 201 n n C37 H34 A1AC8 sing 202 n n N08 H36 A1AC8 sing 203 n n O05 H35 A1AC8 sing 204 n n # _atom_sites.entry_id 8HMB _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 R16 D 1 2301 1701 R16 R16 . E 4 R16 D 1 2302 1704 R16 R16 . F 5 3PE D 1 2303 1705 3PE 3PE . G 4 R16 D 1 2304 1707 R16 R16 . H 4 R16 D 1 2305 1708 R16 R16 . I 4 R16 D 1 2306 1710 R16 R16 . J 5 3PE D 1 2307 1711 3PE 3PE . K 4 R16 D 1 2308 1713 R16 R16 . L 4 R16 D 1 2309 1714 R16 R16 . M 4 R16 D 1 2310 1715 R16 R16 . N 6 A1AC8 D 1 2311 1726 A1AC8 BEN . O 5 3PE D 1 2312 1727 3PE 3PE . P 7 CA D 1 2313 2 CA CA . Q 7 CA D 1 2314 3 CA CA . R 8 NAG E 1 1101 1372 NAG NAG . S 8 NAG E 1 1102 1373 NAG NAG . T 8 NAG E 1 1103 1383 NAG NAG . U 8 NAG E 1 1104 1393 NAG NAG . V 8 NAG E 1 1105 1394 NAG NAG . W 8 NAG E 1 1106 1397 NAG NAG . X 8 NAG E 1 1107 1399 NAG NAG . Y 8 NAG E 1 1108 1400 NAG NAG . # 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 C10 A1AC8 . . . N 6 166.505 163.414 155.575 1 51.7 ? C10 A1AC8 2311 D 1 HETATM 2 C C11 A1AC8 . . . N 6 166.413 162.174 156.449 1 51.7 ? C11 A1AC8 2311 D 1 HETATM 3 C C12 A1AC8 . . . N 6 166.701 162.959 154.134 1 51.7 ? C12 A1AC8 2311 D 1 HETATM 4 C C13 A1AC8 . . . N 6 165.282 161.342 155.867 1 51.7 ? C13 A1AC8 2311 D 1 HETATM 5 C C14 A1AC8 . . . N 6 165.539 161.149 154.377 1 51.7 ? C14 A1AC8 2311 D 1 HETATM 6 C C15 A1AC8 . . . N 6 165.582 162.177 152.438 1 51.7 ? C15 A1AC8 2311 D 1 HETATM 7 C C16 A1AC8 . . . N 6 167.783 167.568 155.66 1 51.7 ? C16 A1AC8 2311 D 1 HETATM 8 C C17 A1AC8 . . . N 6 167.901 166.586 156.832 1 51.7 ? C17 A1AC8 2311 D 1 HETATM 9 C C18 A1AC8 . . . N 6 167.112 165.29 156.762 1 51.7 ? C18 A1AC8 2311 D 1 HETATM 10 C C19 A1AC8 . . . N 6 166.386 161.014 151.846 1 51.7 ? C19 A1AC8 2311 D 1 HETATM 11 C C20 A1AC8 . . . N 6 168.969 167.275 154.722 1 51.7 ? C20 A1AC8 2311 D 1 HETATM 12 C C21 A1AC8 . . . N 6 169.039 166.553 157.473 1 51.7 ? C21 A1AC8 2311 D 1 HETATM 13 C C22 A1AC8 . . . N 6 166.386 167.406 155.053 1 51.7 ? C22 A1AC8 2311 D 1 HETATM 14 C C23 A1AC8 . . . N 6 170.114 167.004 155.281 1 51.7 ? C23 A1AC8 2311 D 1 HETATM 15 C C24 A1AC8 . . . N 6 165.748 159.837 151.482 1 51.7 ? C24 A1AC8 2311 D 1 HETATM 16 C C25 A1AC8 . . . N 6 167.75 161.135 151.638 1 51.7 ? C25 A1AC8 2311 D 1 HETATM 17 C C26 A1AC8 . . . N 6 169.203 165.617 158.666 1 51.7 ? C26 A1AC8 2311 D 1 HETATM 18 C C27 A1AC8 . . . N 6 166.158 166.698 153.89 1 51.7 ? C27 A1AC8 2311 D 1 HETATM 19 C C28 A1AC8 . . . N 6 165.318 167.964 155.723 1 51.7 ? C28 A1AC8 2311 D 1 HETATM 20 C C29 A1AC8 . . . N 6 169.011 167.488 153.209 1 51.7 ? C29 A1AC8 2311 D 1 HETATM 21 C C30 A1AC8 . . . N 6 171.15 166.297 154.422 1 51.7 ? C30 A1AC8 2311 D 1 HETATM 22 C C31 A1AC8 . . . N 6 166.468 158.786 150.944 1 51.7 ? C31 A1AC8 2311 D 1 HETATM 23 C C32 A1AC8 . . . N 6 168.473 160.086 151.1 1 51.7 ? C32 A1AC8 2311 D 1 HETATM 24 C C33 A1AC8 . . . N 6 164.884 166.576 153.381 1 51.7 ? C33 A1AC8 2311 D 1 HETATM 25 C C34 A1AC8 . . . N 6 164.044 167.833 155.211 1 51.7 ? C34 A1AC8 2311 D 1 HETATM 26 C C35 A1AC8 . . . N 6 167.832 158.911 150.751 1 51.7 ? C35 A1AC8 2311 D 1 HETATM 27 C C36 A1AC8 . . . N 6 163.816 167.141 154.04 1 51.7 ? C36 A1AC8 2311 D 1 HETATM 28 C C37 A1AC8 . . . N 6 168.786 166.709 151.001 1 51.7 ? C37 A1AC8 2311 D 1 HETATM 29 N N07 A1AC8 . . . N 6 165.635 162.295 153.75 1 51.7 ? N07 A1AC8 2311 D 1 HETATM 30 N N08 A1AC8 . . . N 6 170.197 166.937 156.718 1 51.7 ? N08 A1AC8 2311 D 1 HETATM 31 N N09 A1AC8 . . . N 6 164.684 165.852 152.149 1 51.7 ? N09 A1AC8 2311 D 1 HETATM 32 O O01 A1AC8 . . . N 6 167.568 164.223 155.985 1 51.7 ? O01 A1AC8 2311 D 1 HETATM 33 O O02 A1AC8 . . . N 6 166.102 165.193 157.368 1 51.7 ? O02 A1AC8 2311 D 1 HETATM 34 O O03 A1AC8 . . . N 6 168.734 166.409 152.362 1 51.7 ? O03 A1AC8 2311 D 1 HETATM 35 O O04 A1AC8 . . . N 6 169.303 168.544 152.762 1 51.7 ? O04 A1AC8 2311 D 1 HETATM 36 O O05 A1AC8 . . . N 6 165.758 165.155 151.587 1 51.7 ? O05 A1AC8 2311 D 1 HETATM 37 O O06 A1AC8 . . . N 6 163.637 165.864 151.62 1 51.7 ? O06 A1AC8 2311 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 37 #