data_6R12 # _model_server_result.job_id HHTIafapxV9NfqjODTlWPg _model_server_result.datetime_utc '2024-10-10 17:21:04' _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":"F","auth_seq_id":202}' # _entry.id 6R12 # _exptl.entry_id 6R12 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 258.229 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-Thalidomide _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 N 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 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 'C13 H10 N2 O4' _chem_comp.formula_weight 258.229 _chem_comp.id EF2 _chem_comp.mon_nstd_flag . _chem_comp.name S-Thalidomide _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 O01 C02 EF2 doub 83 n n C02 N03 EF2 sing 84 n n C02 C08 EF2 sing 85 n n N03 C04 EF2 sing 86 n n C04 O05 EF2 doub 87 n n C04 C06 EF2 sing 88 n n C06 C07 EF2 sing 89 n n C07 C08 EF2 sing 90 n n C08 N09 EF2 sing 91 n n N09 C3 EF2 sing 92 n n N09 C4 EF2 sing 93 n n C11 C12 EF2 sing 94 n y C11 C20 EF2 doub 95 n y C12 C13 EF2 doub 96 n y C13 C14 EF2 sing 97 n y C13 C4 EF2 sing 98 n n C14 C19 EF2 doub 99 n y C14 C3 EF2 sing 100 n n O16 C4 EF2 doub 101 n n O18 C3 EF2 doub 102 n n C19 C20 EF2 sing 103 n y N03 H03 EF2 sing 104 n n C08 H08 EF2 sing 105 n n C06 H061 EF2 sing 106 n n C06 H062 EF2 sing 107 n n C07 H071 EF2 sing 108 n n C07 H072 EF2 sing 109 n n C11 H11 EF2 sing 110 n n C12 H12 EF2 sing 111 n n C20 H20 EF2 sing 112 n n C19 H19 EF2 sing 113 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 O O01 EF2 . . . F 4 25.776 15.994 -8.657 1 24.85 ? O01 EF2 202 A 1 HETATM 2 C C02 EF2 . . . F 4 24.822 16.457 -8.069 1 24.04 ? C02 EF2 202 A 1 HETATM 3 N N03 EF2 . . . F 4 23.597 15.829 -8.097 1 23.54 ? N03 EF2 202 A 1 HETATM 4 C C04 EF2 . . . F 4 22.44 16.242 -7.468 1 21.81 ? C04 EF2 202 A 1 HETATM 5 O O05 EF2 . . . F 4 21.453 15.532 -7.474 1 21.3 ? O05 EF2 202 A 1 HETATM 6 C C06 EF2 . . . F 4 22.463 17.576 -6.792 1 22.28 ? C06 EF2 202 A 1 HETATM 7 C C07 EF2 . . . F 4 23.563 18.491 -7.294 1 23.6 ? C07 EF2 202 A 1 HETATM 8 C C08 EF2 . . . F 4 24.889 17.751 -7.261 1 24.17 ? C08 EF2 202 A 1 HETATM 9 N N09 EF2 . . . F 4 26 18.553 -7.742 1 27.74 ? N09 EF2 202 A 1 HETATM 10 C C11 EF2 . . . F 4 29.857 20.916 -8.65 1 33.54 ? C11 EF2 202 A 1 HETATM 11 C C12 EF2 . . . F 4 29.197 20.321 -7.583 1 33.04 ? C12 EF2 202 A 1 HETATM 12 C C13 EF2 . . . F 4 27.988 19.714 -7.846 1 31.65 ? C13 EF2 202 A 1 HETATM 13 C C14 EF2 . . . F 4 27.449 19.696 -9.121 1 31.25 ? C14 EF2 202 A 1 HETATM 14 O O16 EF2 . . . F 4 27.141 18.823 -5.744 1 27.21 ? O16 EF2 202 A 1 HETATM 15 O O18 EF2 . . . F 4 25.362 18.764 -9.958 1 30.76 ? O18 EF2 202 A 1 HETATM 16 C C19 EF2 . . . F 4 28.098 20.285 -10.185 1 34.75 ? C19 EF2 202 A 1 HETATM 17 C C20 EF2 . . . F 4 29.317 20.898 -9.928 1 36.2 ? C20 EF2 202 A 1 HETATM 18 C C3 EF2 . . . F 4 26.153 18.972 -9.068 1 28.99 ? C3 EF2 202 A 1 HETATM 19 C C4 EF2 . . . F 4 27.053 19.002 -6.937 1 28.9 ? C4 EF2 202 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #