data_6R12 # _model_server_result.job_id Su-lD28EoGyT9tm4qd5cQw _model_server_result.datetime_utc '2024-12-04 15:54:25' _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 6r12 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":202}' # _entry.id 6R12 # _exptl.entry_id 6R12 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 232.235 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2-phenyl-ethanamide _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 6R12 _cell.length_a 56.417 _cell.length_b 58.795 _cell.length_c 88.234 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6R12 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,O 1 1 B,H,I,J,K,L,P 2 1 C,M,N,Q 3 1 D,R 3 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_445 x-1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 -28.2085 -29.3975 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id I _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 metalc ? metalc1 A SG CYS 25 A CYS 24 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc2 A SG CYS 28 A CYS 27 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc3 A SG CYS 91 A CYS 90 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc4 A SG CYS 94 A CYS 93 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc5 B SG CYS 25 B CYS 24 1_555 H ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc6 B SG CYS 28 B CYS 27 1_555 H ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc7 B SG CYS 91 B CYS 90 1_555 H ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc8 B SG CYS 94 B CYS 93 1_555 H ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc9 C SG CYS 25 C CYS 24 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc10 C SG CYS 28 C CYS 27 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc11 C SG CYS 91 C CYS 90 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc12 C SG CYS 94 C CYS 93 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? # _chem_comp.formula 'C12 H12 N2 O3' _chem_comp.formula_weight 232.235 _chem_comp.id JOT _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2-phenyl-ethanamide _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 O1 C1 JOT doub 204 n n N1 C1 JOT sing 205 n n N1 C4 JOT sing 206 n n C1 C2 JOT sing 207 n n C4 O2 JOT doub 208 n n C4 C3 JOT sing 209 n n C2 C3 JOT sing 210 n n C3 N2 JOT sing 211 n n O3 C5 JOT doub 212 n n N2 C5 JOT sing 213 n n C5 C6 JOT sing 214 n n C6 C7 JOT sing 215 n n C7 C8 JOT doub 216 n y C7 C12 JOT sing 217 n y C8 C9 JOT sing 218 n y C12 C11 JOT doub 219 n y C9 C10 JOT doub 220 n y C11 C10 JOT sing 221 n y C6 H1 JOT sing 222 n n C6 H2 JOT sing 223 n n C11 H3 JOT sing 224 n n C8 H4 JOT sing 225 n n C9 H5 JOT sing 226 n n C10 H6 JOT sing 227 n n C12 H7 JOT sing 228 n n N1 H8 JOT sing 229 n n N2 H9 JOT sing 230 n n C3 H10 JOT sing 231 n n C2 H11 JOT sing 232 n n C2 H12 JOT sing 233 n n # _atom_sites.entry_id 6R12 _atom_sites.fract_transf_matrix[1][1] 0.017725 _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] 0.017008 _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] 0.011334 _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 E 3 ZN A 1 201 201 ZN ZN . F 4 EF2 A 1 202 202 EF2 EF2 . G 5 PO4 A 1 203 203 PO4 PO4 . H 3 ZN B 1 201 201 ZN ZN . I 6 JOT B 1 202 202 JOT JOT . J 5 PO4 B 1 203 203 PO4 PO4 . K 7 CL B 1 204 204 CL CL . L 7 CL B 1 205 205 CL CL . M 3 ZN C 1 201 201 ZN ZN . N 4 EF2 C 1 202 202 EF2 EF2 . O 8 HOH A 1 301 301 HOH HOH . O 8 HOH A 2 302 306 HOH HOH . O 8 HOH A 3 303 302 HOH HOH . O 8 HOH A 4 304 305 HOH HOH . O 8 HOH A 5 305 304 HOH HOH . O 8 HOH A 6 306 303 HOH HOH . O 8 HOH A 7 307 313 HOH HOH . O 8 HOH A 8 308 312 HOH HOH . O 8 HOH A 9 309 314 HOH HOH . O 8 HOH A 10 310 310 HOH HOH . O 8 HOH A 11 311 325 HOH HOH . O 8 HOH A 12 312 309 HOH HOH . O 8 HOH A 13 313 308 HOH HOH . O 8 HOH A 14 314 316 HOH HOH . O 8 HOH A 15 315 307 HOH HOH . O 8 HOH A 16 316 327 HOH HOH . O 8 HOH A 17 317 322 HOH HOH . O 8 HOH A 18 318 315 HOH HOH . O 8 HOH A 19 319 321 HOH HOH . O 8 HOH A 20 320 324 HOH HOH . O 8 HOH A 21 321 319 HOH HOH . O 8 HOH A 22 322 318 HOH HOH . O 8 HOH A 23 323 323 HOH HOH . O 8 HOH A 24 324 326 HOH HOH . O 8 HOH A 25 325 330 HOH HOH . O 8 HOH A 26 326 345 HOH HOH . O 8 HOH A 27 327 317 HOH HOH . O 8 HOH A 28 328 311 HOH HOH . O 8 HOH A 29 329 331 HOH HOH . O 8 HOH A 30 330 329 HOH HOH . O 8 HOH A 31 331 328 HOH HOH . O 8 HOH A 32 332 320 HOH HOH . O 8 HOH A 33 333 340 HOH HOH . O 8 HOH A 34 334 347 HOH HOH . O 8 HOH A 35 335 338 HOH HOH . O 8 HOH A 36 336 341 HOH HOH . O 8 HOH A 37 337 333 HOH HOH . O 8 HOH A 38 338 334 HOH HOH . O 8 HOH A 39 339 336 HOH HOH . O 8 HOH A 40 340 343 HOH HOH . O 8 HOH A 41 341 337 HOH HOH . O 8 HOH A 42 342 335 HOH HOH . O 8 HOH A 43 343 332 HOH HOH . O 8 HOH A 44 344 342 HOH HOH . O 8 HOH A 45 345 353 HOH HOH . O 8 HOH A 46 346 344 HOH HOH . O 8 HOH A 47 347 339 HOH HOH . O 8 HOH A 48 348 348 HOH HOH . O 8 HOH A 49 349 354 HOH HOH . O 8 HOH A 50 350 351 HOH HOH . O 8 HOH A 51 351 356 HOH HOH . O 8 HOH A 52 352 350 HOH HOH . O 8 HOH A 53 353 346 HOH HOH . O 8 HOH A 54 354 355 HOH HOH . O 8 HOH A 55 355 349 HOH HOH . O 8 HOH A 56 356 361 HOH HOH . O 8 HOH A 57 357 360 HOH HOH . O 8 HOH A 58 358 357 HOH HOH . O 8 HOH A 59 359 358 HOH HOH . O 8 HOH A 60 360 359 HOH HOH . O 8 HOH A 61 361 362 HOH HOH . O 8 HOH A 62 362 364 HOH HOH . O 8 HOH A 63 363 363 HOH HOH . O 8 HOH A 64 364 366 HOH HOH . O 8 HOH A 65 365 365 HOH HOH . O 8 HOH A 66 366 367 HOH HOH . O 8 HOH A 67 367 368 HOH HOH . O 8 HOH A 68 368 371 HOH HOH . O 8 HOH A 69 369 369 HOH HOH . O 8 HOH A 70 370 370 HOH HOH . O 8 HOH A 71 371 372 HOH HOH . O 8 HOH A 72 372 374 HOH HOH . O 8 HOH A 73 373 373 HOH HOH . O 8 HOH A 74 374 375 HOH HOH . O 8 HOH A 75 375 376 HOH HOH . P 8 HOH B 1 301 301 HOH HOH . P 8 HOH B 2 302 302 HOH HOH . P 8 HOH B 3 303 303 HOH HOH . P 8 HOH B 4 304 343 HOH HOH . P 8 HOH B 5 305 305 HOH HOH . P 8 HOH B 6 306 349 HOH HOH . P 8 HOH B 7 307 304 HOH HOH . P 8 HOH B 8 308 307 HOH HOH . P 8 HOH B 9 309 306 HOH HOH . P 8 HOH B 10 310 308 HOH HOH . P 8 HOH B 11 311 321 HOH HOH . P 8 HOH B 12 312 336 HOH HOH . P 8 HOH B 13 313 319 HOH HOH . P 8 HOH B 14 314 310 HOH HOH . P 8 HOH B 15 315 309 HOH HOH . P 8 HOH B 16 316 311 HOH HOH . P 8 HOH B 17 317 318 HOH HOH . P 8 HOH B 18 318 315 HOH HOH . P 8 HOH B 19 319 314 HOH HOH . P 8 HOH B 20 320 323 HOH HOH . P 8 HOH B 21 321 333 HOH HOH . P 8 HOH B 22 322 325 HOH HOH . P 8 HOH B 23 323 326 HOH HOH . P 8 HOH B 24 324 313 HOH HOH . P 8 HOH B 25 325 316 HOH HOH . P 8 HOH B 26 326 344 HOH HOH . P 8 HOH B 27 327 320 HOH HOH . P 8 HOH B 28 328 328 HOH HOH . P 8 HOH B 29 329 322 HOH HOH . P 8 HOH B 30 330 312 HOH HOH . P 8 HOH B 31 331 324 HOH HOH . P 8 HOH B 32 332 330 HOH HOH . P 8 HOH B 33 333 329 HOH HOH . P 8 HOH B 34 334 337 HOH HOH . P 8 HOH B 35 335 335 HOH HOH . P 8 HOH B 36 336 331 HOH HOH . P 8 HOH B 37 337 338 HOH HOH . P 8 HOH B 38 338 339 HOH HOH . P 8 HOH B 39 339 340 HOH HOH . P 8 HOH B 40 340 332 HOH HOH . P 8 HOH B 41 341 317 HOH HOH . P 8 HOH B 42 342 348 HOH HOH . P 8 HOH B 43 343 334 HOH HOH . P 8 HOH B 44 344 341 HOH HOH . P 8 HOH B 45 345 345 HOH HOH . P 8 HOH B 46 346 352 HOH HOH . P 8 HOH B 47 347 347 HOH HOH . P 8 HOH B 48 348 350 HOH HOH . P 8 HOH B 49 349 351 HOH HOH . P 8 HOH B 50 350 346 HOH HOH . P 8 HOH B 51 351 342 HOH HOH . P 8 HOH B 52 352 353 HOH HOH . P 8 HOH B 53 353 327 HOH HOH . P 8 HOH B 54 354 354 HOH HOH . P 8 HOH B 55 355 352 HOH HOH . P 8 HOH B 56 356 357 HOH HOH . P 8 HOH B 57 357 356 HOH HOH . P 8 HOH B 58 358 358 HOH HOH . P 8 HOH B 59 359 360 HOH HOH . P 8 HOH B 60 360 359 HOH HOH . P 8 HOH B 61 361 362 HOH HOH . P 8 HOH B 62 362 361 HOH HOH . P 8 HOH B 63 363 365 HOH HOH . P 8 HOH B 64 364 363 HOH HOH . P 8 HOH B 65 365 366 HOH HOH . P 8 HOH B 66 366 367 HOH HOH . P 8 HOH B 67 367 355 HOH HOH . P 8 HOH B 68 368 364 HOH HOH . P 8 HOH B 69 369 368 HOH HOH . P 8 HOH B 70 370 371 HOH HOH . P 8 HOH B 71 371 370 HOH HOH . P 8 HOH B 72 372 369 HOH HOH . P 8 HOH B 73 373 372 HOH HOH . P 8 HOH B 74 374 373 HOH HOH . P 8 HOH B 75 375 374 HOH HOH . P 8 HOH B 76 376 375 HOH HOH . P 8 HOH B 77 377 376 HOH HOH . P 8 HOH B 78 378 377 HOH HOH . P 8 HOH B 79 379 378 HOH HOH . Q 8 HOH C 1 301 302 HOH HOH . Q 8 HOH C 2 302 306 HOH HOH . Q 8 HOH C 3 303 309 HOH HOH . Q 8 HOH C 4 304 305 HOH HOH . Q 8 HOH C 5 305 301 HOH HOH . Q 8 HOH C 6 306 303 HOH HOH . Q 8 HOH C 7 307 307 HOH HOH . Q 8 HOH C 8 308 304 HOH HOH . Q 8 HOH C 9 309 317 HOH HOH . Q 8 HOH C 10 310 313 HOH HOH . Q 8 HOH C 11 311 320 HOH HOH . Q 8 HOH C 12 312 308 HOH HOH . Q 8 HOH C 13 313 314 HOH HOH . Q 8 HOH C 14 314 312 HOH HOH . Q 8 HOH C 15 315 322 HOH HOH . Q 8 HOH C 16 316 316 HOH HOH . Q 8 HOH C 17 317 310 HOH HOH . Q 8 HOH C 18 318 315 HOH HOH . Q 8 HOH C 19 319 311 HOH HOH . Q 8 HOH C 20 320 318 HOH HOH . Q 8 HOH C 21 321 321 HOH HOH . Q 8 HOH C 22 322 323 HOH HOH . Q 8 HOH C 23 323 324 HOH HOH . Q 8 HOH C 24 324 319 HOH HOH . Q 8 HOH C 25 325 325 HOH HOH . Q 8 HOH C 26 326 327 HOH HOH . Q 8 HOH C 27 327 328 HOH HOH . Q 8 HOH C 28 328 326 HOH HOH . Q 8 HOH C 29 329 330 HOH HOH . Q 8 HOH C 30 330 329 HOH HOH . Q 8 HOH C 31 331 332 HOH HOH . Q 8 HOH C 32 332 331 HOH HOH . Q 8 HOH C 33 333 334 HOH HOH . Q 8 HOH C 34 334 333 HOH HOH . Q 8 HOH C 35 335 335 HOH HOH . R 8 HOH F 1 101 101 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 C4 JOT . . . I 6 22.415 13.993 26.165 1 22.51 ? C4 JOT 202 B 1 HETATM 2 C C5 JOT . . . I 6 24.448 15.509 28.226 1 28.13 ? C5 JOT 202 B 1 HETATM 3 C C6 JOT . . . I 6 24.31 15.992 29.653 1 30.69 ? C6 JOT 202 B 1 HETATM 4 C C11 JOT . . . I 6 21.159 18.088 29.973 1 39.08 ? C11 JOT 202 B 1 HETATM 5 C C7 JOT . . . I 6 23.38 17.177 29.751 1 31.37 ? C7 JOT 202 B 1 HETATM 6 C C8 JOT . . . I 6 23.872 18.473 29.711 1 37.72 ? C8 JOT 202 B 1 HETATM 7 C C9 JOT . . . I 6 23.016 19.559 29.801 1 38.84 ? C9 JOT 202 B 1 HETATM 8 C C10 JOT . . . I 6 21.663 19.364 29.932 1 39.01 ? C10 JOT 202 B 1 HETATM 9 C C12 JOT . . . I 6 22.012 16.998 29.883 1 34.54 ? C12 JOT 202 B 1 HETATM 10 N N1 JOT . . . I 6 21.943 12.823 25.64 1 21.14 ? N1 JOT 202 B 1 HETATM 11 N N2 JOT . . . I 6 23.989 14.278 27.995 1 24.91 ? N2 JOT 202 B 1 HETATM 12 C C3 JOT . . . I 6 23.823 13.754 26.667 1 22.2 ? C3 JOT 202 B 1 HETATM 13 C C1 JOT . . . I 6 22.821 11.773 25.775 1 19.33 ? C1 JOT 202 B 1 HETATM 14 C C2 JOT . . . I 6 23.979 12.23 26.617 1 20.46 ? C2 JOT 202 B 1 HETATM 15 O O1 JOT . . . I 6 22.655 10.672 25.279 1 18.72 ? O1 JOT 202 B 1 HETATM 16 O O2 JOT . . . I 6 21.806 15.045 26.219 1 23.78 ? O2 JOT 202 B 1 HETATM 17 O O3 JOT . . . I 6 24.947 16.198 27.335 1 26.4 ? O3 JOT 202 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 17 #