data_6JP5 # _model_server_result.job_id AyjyrxlLobTqQmC3zgcRng _model_server_result.datetime_utc '2024-10-11 00:32:32' _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 6jp5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":1911}' # _entry.id 6JP5 # _exptl.entry_id 6JP5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 346.335 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-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 6JP5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JP5 _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details 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,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA _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 10 _struct_asym.id W _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 5 2 1 NAG NAG C1 O1 . O3 HO3 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 5 n F NAG 1 D 1 NAG F 1201 NAG 5 n F NAG 2 D 2 NAG F 1202 NAG 5 n G NAG 1 G 1 NAG F 1204 NAG 5 n G NAG 2 G 2 NAG F 1205 NAG 6 n H NAG 1 H 1 NAG F 1209 NAG 6 n H NAG 2 H 2 NAG F 1208 NAG 6 n H BMA 3 H 3 BMA F 1207 BMA 6 n I NAG 1 I 1 NAG F 1210 NAG 6 n I NAG 2 I 2 NAG F 1211 NAG 6 n I BMA 3 I 3 BMA F 1212 BMA 5 n J NAG 1 J 1 NAG F 1215 NAG 5 n J NAG 2 J 2 NAG F 1216 NAG 5 n K NAG 1 K 1 NAG F 1217 NAG 5 n K NAG 2 K 2 NAG F 1218 NAG 5 n L NAG 1 L 1 NAG F 1223 NAG 5 n L NAG 2 L 2 NAG F 1222 NAG # 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 226 A CYS 226 1_555 A SG CYS 254 A CYS 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? disulf ? disulf2 A SG CYS 957 A CYS 957 1_555 A SG CYS 968 A CYS 968 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf3 A SG CYS 1338 A CYS 1338 1_555 A SG CYS 1352 A CYS 1352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? disulf ? disulf4 B SG CYS 57 E CYS 57 1_555 B SG CYS 80 E CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 C SG CYS 305 F CYS 305 1_555 C SG CYS 1046 F CYS 1047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 C SG CYS 356 F CYS 356 1_555 C SG CYS 1061 F CYS 1062 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? disulf ? disulf7 C SG CYS 406 F CYS 406 1_555 C SG CYS 1073 F CYS 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? disulf ? disulf8 C SG CYS 669 F CYS 670 1_555 C SG CYS 699 F CYS 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf9 C SG CYS 906 F CYS 907 1_555 C SG CYS 976 F CYS 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 998 F CYS 999 1_555 C SG CYS 1028 F CYS 1029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf11 C SG CYS 1001 F CYS 1002 1_555 C SG CYS 1026 F CYS 1027 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? covale ? covale1 A ND2 ASN 257 A ASN 257 1_555 M C1 NAG . A NAG 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? covale ? covale2 C ND2 ASN 94 F ASN 92 1_555 DA C1 NAG . F NAG 1114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 C ND2 ASN 186 F ASN 186 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 C ND2 ASN 470 F ASN 470 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.555 ? covale ? covale5 C ND2 ASN 606 F ASN 606 1_555 EA C1 NAG . F NAG 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale6 C ND2 ASN 615 F ASN 615 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.529 ? covale ? covale7 C ND2 ASN 826 F ASN 827 1_555 IA C1 NAG . F NAG 1125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale8 C ND2 ASN 890 F ASN 891 1_555 CA C1 NAG . F NAG 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale9 C ND2 ASN 897 F ASN 898 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale10 F O3 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale15 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale17 K O3 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale18 L O3 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A OD2 ASP 78 A ASP 78 1_555 Z CA CA . A CA 1914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc2 A OE1 GLU 292 A GLU 292 1_555 N CA CA . A CA 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? metalc ? metalc3 A OE2 GLU 292 A GLU 292 1_555 N CA CA . A CA 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc4 A OE1 GLU 292 A GLU 292 1_555 O CA CA . A CA 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? metalc ? metalc5 A OE1 GLU 1014 A GLU 1014 1_555 N CA CA . A CA 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc6 A OE2 GLU 1014 A GLU 1014 1_555 N CA CA . A CA 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc7 A OE2 GLU 1014 A GLU 1014 1_555 O CA CA . A CA 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? metalc ? metalc8 Z CA CA . A CA 1914 1_555 C OG SER 263 F SER 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc9 Z CA CA . A CA 1914 1_555 C OG SER 265 F SER 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc10 Z CA CA . A CA 1914 1_555 C OG1 THR 333 F THR 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _chem_comp.formula 'C17 H18 N2 O6' _chem_comp.formula_weight 346.335 _chem_comp.id C5U _chem_comp.mon_nstd_flag . _chem_comp.name 'dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-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 C13 O12 C5U sing 226 n n O12 C10 C5U sing 227 n n O11 C10 C5U doub 228 n n C18 C17 C5U sing 229 n y C18 C19 C5U doub 230 n y C17 C16 C5U doub 231 n y C10 C09 C5U sing 232 n n C19 C20 C5U sing 233 n y C16 C15 C5U sing 234 n y C20 C15 C5U doub 235 n y C20 N21 C5U sing 236 n n C24 C08 C5U sing 237 n n C15 C14 C5U sing 238 n n C09 C08 C5U doub 239 n n C09 C14 C5U sing 240 n n N21 O22 C5U sing 241 n n N21 O23 C5U doub 242 n n C08 N07 C5U sing 243 n n C14 C05 C5U sing 244 n n C05 C06 C5U doub 245 n n C05 C02 C5U sing 246 n n N07 C06 C5U sing 247 n n O03 C02 C5U sing 248 n n O03 C04 C5U sing 249 n n C06 C25 C5U sing 250 n n C02 O01 C5U doub 251 n n C13 H1 C5U sing 252 n n C13 H2 C5U sing 253 n n C13 H3 C5U sing 254 n n C17 H4 C5U sing 255 n n C24 H5 C5U sing 256 n n C24 H6 C5U sing 257 n n C24 H7 C5U sing 258 n n C04 H8 C5U sing 259 n n C04 H9 C5U sing 260 n n C04 H10 C5U sing 261 n n N07 H13 C5U sing 262 n n C14 H17 C5U sing 263 n n C16 H18 C5U sing 264 n n C18 H19 C5U sing 265 n n C19 H20 C5U sing 266 n n C25 H21 C5U sing 267 n n C25 H22 C5U sing 268 n n C25 H23 C5U sing 269 n n # _atom_sites.entry_id 6JP5 _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 M 7 NAG A 1 1901 1901 NAG NAG . N 8 CA A 1 1902 1902 CA CA . O 8 CA A 1 1903 1903 CA CA . P 9 3PE A 1 1904 10 3PE 3PE . Q 9 3PE A 1 1905 11 3PE 3PE . R 9 3PE A 1 1906 12 3PE 3PE . S 9 3PE A 1 1907 13 3PE 3PE . T 9 3PE A 1 1908 14 3PE 3PE . U 9 3PE A 1 1909 15 3PE 3PE . V 9 3PE A 1 1910 16 3PE 3PE . W 10 C5U A 1 1911 6 C5U LIG . X 11 PC1 A 1 1912 1 PC1 PC1 . Y 9 3PE A 1 1913 2 3PE 3PE . Z 8 CA A 1 1914 1904 CA CA . AA 12 ETA F 1 1101 1075 ETA ETA . BA 7 NAG F 1 1104 1203 NAG NAG . CA 7 NAG F 1 1107 1206 NAG NAG . DA 7 NAG F 1 1114 1213 NAG NAG . EA 7 NAG F 1 1115 1214 NAG NAG . FA 7 NAG F 1 1120 1219 NAG NAG . GA 7 NAG F 1 1121 1220 NAG NAG . HA 7 NAG F 1 1122 1221 NAG NAG . IA 7 NAG F 1 1125 1224 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 C5U . . . W 10 166.201 193.079 173.85 1 20 ? C10 C5U 1911 A 1 HETATM 2 C C13 C5U . . . W 10 164.995 193.699 171.95 1 20 ? C13 C5U 1911 A 1 HETATM 3 C C15 C5U . . . W 10 163.568 194.406 175.067 1 20 ? C15 C5U 1911 A 1 HETATM 4 C C17 C5U . . . W 10 161.607 193.961 173.739 1 20 ? C17 C5U 1911 A 1 HETATM 5 C C20 C5U . . . W 10 163.37 195.776 174.9 1 20 ? C20 C5U 1911 A 1 HETATM 6 C C24 C5U . . . W 10 166.271 190.245 175.043 1 20 ? C24 C5U 1911 A 1 HETATM 7 O O01 C5U . . . W 10 162.698 194.037 178.977 1 20 ? O01 C5U 1911 A 1 HETATM 8 C C02 C5U . . . W 10 163.323 194.431 178.056 1 20 ? C02 C5U 1911 A 1 HETATM 9 O O03 C5U . . . W 10 163.276 195.786 177.686 1 20 ? O03 C5U 1911 A 1 HETATM 10 C C04 C5U . . . W 10 162.919 196.656 178.738 1 20 ? C04 C5U 1911 A 1 HETATM 11 C C05 C5U . . . W 10 164.198 193.449 177.268 1 20 ? C05 C5U 1911 A 1 HETATM 12 C C06 C5U . . . W 10 164.814 192.266 178.005 1 20 ? C06 C5U 1911 A 1 HETATM 13 N N07 C5U . . . W 10 165.704 191.394 177.275 1 20 ? N07 C5U 1911 A 1 HETATM 14 C C08 C5U . . . W 10 165.702 191.437 175.837 1 20 ? C08 C5U 1911 A 1 HETATM 15 C C09 C5U . . . W 10 165.414 192.754 175.129 1 20 ? C09 C5U 1911 A 1 HETATM 16 O O11 C5U . . . W 10 167.143 192.431 173.558 1 20 ? O11 C5U 1911 A 1 HETATM 17 O O12 C5U . . . W 10 165.8 194.134 173.025 1 20 ? O12 C5U 1911 A 1 HETATM 18 C C14 C5U . . . W 10 164.758 193.892 175.913 1 20 ? C14 C5U 1911 A 1 HETATM 19 C C16 C5U . . . W 10 162.683 193.501 174.493 1 20 ? C16 C5U 1911 A 1 HETATM 20 C C18 C5U . . . W 10 161.417 195.33 173.569 1 20 ? C18 C5U 1911 A 1 HETATM 21 C C19 C5U . . . W 10 162.295 196.239 174.151 1 20 ? C19 C5U 1911 A 1 HETATM 22 N N21 C5U . . . W 10 164.293 196.729 175.512 1 20 ? N21 C5U 1911 A 1 HETATM 23 O O22 C5U . . . W 10 165.652 196.422 175.614 1 20 ? O22 C5U 1911 A 1 HETATM 24 O O23 C5U . . . W 10 163.893 197.756 175.92 1 20 ? O23 C5U 1911 A 1 HETATM 25 C C25 C5U . . . W 10 164.11 191.742 179.267 1 20 ? C25 C5U 1911 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 25 #