data_3L75 # _model_server_result.job_id YvDc3loOpsp4wHBMaDqwKA _model_server_result.datetime_utc '2024-11-05 11:03:41' _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 3l75 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":2001}' # _entry.id 3L75 # _exptl.entry_id 3L75 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 311.401 _entity.id 14 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one _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 3L75 _cell.length_a 172.285 _cell.length_b 182.141 _cell.length_c 241.198 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L75 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 14 Y N N ? 14 SA 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 disulf ? disulf1 E SG CYS 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 H SG CYS 23 H CYS 24 1_555 H SG CYS 67 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf3 H SG CYS 39 H CYS 40 1_555 H SG CYS 53 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf4 O SG CYS 144 R CYS 144 1_555 O SG CYS 160 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 R SG CYS 23 U CYS 24 1_555 R SG CYS 67 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 R SG CYS 39 U CYS 40 1_555 R SG CYS 53 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc1 C NE2 HIS 84 C HIS 84 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc2 C NE2 HIS 98 C HIS 98 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc5 D NE2 HIS 41 D HIS 41 1_555 HA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc6 D SD MET 160 D MET 160 1_555 HA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc7 E SG CYS 139 E CYS 139 1_555 MA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc8 E ND1 HIS 141 E HIS 141 1_555 MA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc9 E SG CYS 158 E CYS 158 1_555 MA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc10 E ND1 HIS 161 E HIS 161 1_555 MA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc11 M NE2 HIS 84 P HIS 84 1_555 PA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc12 M NE2 HIS 98 P HIS 98 1_555 QA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc13 M NE2 HIS 183 P HIS 183 1_555 PA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc14 M NE2 HIS 197 P HIS 197 1_555 QA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc15 N NE2 HIS 41 Q HIS 41 1_555 CB FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc16 N SD MET 160 Q MET 160 1_555 CB FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc17 O SG CYS 139 R CYS 139 1_555 GB FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc18 O ND1 HIS 141 R HIS 141 1_555 GB FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc19 O SG CYS 158 R CYS 158 1_555 GB FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc20 O ND1 HIS 161 R HIS 161 1_555 GB FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? # _chem_comp.formula 'C17 H17 N3 O S' _chem_comp.formula_weight 311.401 _chem_comp.id FNM _chem_comp.mon_nstd_flag . _chem_comp.name (5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one _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 N1 N2 FNM sing 392 n n N1 C21 FNM sing 393 n n N2 C3 FNM sing 394 n n N2 C6 FNM sing 395 n n C3 S3 FNM sing 396 n n C3 N4 FNM doub 397 n n S3 C27 FNM sing 398 n n N4 C5 FNM sing 399 n n C5 C6 FNM sing 400 n n C5 C7 FNM sing 401 n n C5 C8 FNM sing 402 n n C6 O6 FNM doub 403 n n C8 C9 FNM doub 404 n y C8 C13 FNM sing 405 n y C9 C10 FNM sing 406 n y C10 C11 FNM doub 407 n y C11 C12 FNM sing 408 n y C12 C13 FNM doub 409 n y C21 C22 FNM doub 410 n y C21 C26 FNM sing 411 n y C22 C23 FNM sing 412 n y C23 C24 FNM doub 413 n y C24 C25 FNM sing 414 n y C25 C26 FNM doub 415 n y N1 HN1 FNM sing 416 n n C7 H7 FNM sing 417 n n C7 H7A FNM sing 418 n n C7 H7B FNM sing 419 n n C9 H9 FNM sing 420 n n C10 H10 FNM sing 421 n n C11 H11 FNM sing 422 n n C12 H12 FNM sing 423 n n C13 H13 FNM sing 424 n n C22 H22 FNM sing 425 n n C23 H23 FNM sing 426 n n C24 H24 FNM sing 427 n n C25 H25 FNM sing 428 n n C26 H26 FNM sing 429 n n C27 H27 FNM sing 430 n n C27 H27A FNM sing 431 n n C27 H27B FNM sing 432 n n # _atom_sites.entry_id 3L75 _atom_sites.fract_transf_matrix[1][1] 0.005804 _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] 0.00549 _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] 0.004146 _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 U 11 PEE A 1 2008 2008 PEE PEE . V 12 UNL A 1 3015 3015 UNL UNL . W 13 HEM C 1 501 501 HEM HEM . X 13 HEM C 1 502 502 HEM HEM . Y 14 FNM C 1 2001 2001 FNM FNM . Z 15 UQ C 1 2002 2002 UQ UQ . AA 11 PEE C 1 2005 2005 PEE PEE . BA 11 PEE C 1 2007 2007 PEE PEE . CA 16 AZI C 1 2011 2011 AZI AZI . DA 12 UNL C 1 2047 2047 UNL UNL . EA 12 UNL C 1 2046 2046 UNL UNL . FA 12 UNL C 1 2048 2048 UNL UNL . GA 17 BOG C 1 3010 3010 BOG BOG . HA 18 HEC D 1 501 501 HEC HEC . IA 19 CDL D 1 2003 2003 CDL CDL . JA 17 BOG D 1 2009 2009 BOG BOG . KA 17 BOG D 1 2091 2091 BOG BOG . LA 12 UNL D 1 2012 2012 UNL UNL . MA 20 FES E 1 501 501 FES FES . NA 19 CDL G 1 2004 2004 CDL CDL . OA 11 PEE N 1 3008 3008 PEE PEE . PA 13 HEM P 1 501 501 HEM HEM . QA 13 HEM P 1 502 502 HEM HEM . RA 17 BOG P 1 2010 2010 BOG BOG . SA 14 FNM P 1 3001 3001 FNM FNM . TA 15 UQ P 1 3002 3002 UQ UQ . UA 11 PEE P 1 3005 3005 PEE PEE . VA 11 PEE P 1 3007 3007 PEE PEE . WA 16 AZI P 1 3011 3011 AZI AZI . XA 12 UNL P 1 3013 3013 UNL UNL . YA 12 UNL P 1 3014 3014 UNL UNL . ZA 12 UNL P 1 3047 3047 UNL UNL . AB 12 UNL P 1 3046 3046 UNL UNL . BB 12 UNL P 1 3048 3048 UNL UNL . CB 18 HEC Q 1 501 501 HEC HEC . DB 19 CDL Q 1 3003 3003 CDL CDL . EB 17 BOG Q 1 3009 3009 BOG BOG . FB 17 BOG Q 1 3091 3091 BOG BOG . GB 20 FES R 1 501 501 FES FES . HB 12 UNL R 1 3012 3012 UNL UNL . IB 19 CDL T 1 3004 3004 CDL CDL . JB 21 HOH A 1 1231 1231 HOH HOH . JB 21 HOH A 2 1284 1284 HOH HOH . KB 21 HOH C 1 381 2 HOH HOH . KB 21 HOH C 2 382 45 HOH HOH . KB 21 HOH C 3 383 47 HOH HOH . KB 21 HOH C 4 384 108 HOH HOH . KB 21 HOH C 5 385 119 HOH HOH . KB 21 HOH C 6 386 168 HOH HOH . KB 21 HOH C 7 387 222 HOH HOH . KB 21 HOH C 8 1008 1008 HOH HOH . KB 21 HOH C 9 1288 1288 HOH HOH . LB 21 HOH E 1 197 5 HOH HOH . LB 21 HOH E 2 198 6 HOH HOH . LB 21 HOH E 3 1289 1289 HOH HOH . MB 21 HOH P 1 381 1 HOH HOH . MB 21 HOH P 2 382 28 HOH HOH . MB 21 HOH P 3 383 35 HOH HOH . MB 21 HOH P 4 384 55 HOH HOH . MB 21 HOH P 5 385 57 HOH HOH . MB 21 HOH P 6 386 109 HOH HOH . MB 21 HOH P 7 387 214 HOH HOH . MB 21 HOH P 8 959 959 HOH HOH . MB 21 HOH P 9 1285 1285 HOH HOH . MB 21 HOH P 10 1286 1286 HOH HOH . NB 21 HOH R 1 197 3 HOH HOH . NB 21 HOH R 2 198 4 HOH HOH . NB 21 HOH R 3 1230 1230 HOH HOH . NB 21 HOH R 4 1287 1287 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 N N1 FNM . . . Y 14 9.341 135.644 78.799 1 41.07 ? N1 FNM 2001 C 1 HETATM 2 N N2 FNM . . . Y 14 10.491 134.883 79.085 1 42.86 ? N2 FNM 2001 C 1 HETATM 3 C C3 FNM . . . Y 14 11.426 135.258 79.956 1 41.95 ? C3 FNM 2001 C 1 HETATM 4 S S3 FNM . . . Y 14 11.318 136.745 80.834 1 40.44 ? S3 FNM 2001 C 1 HETATM 5 N N4 FNM . . . Y 14 12.427 134.378 80.064 1 40.56 ? N4 FNM 2001 C 1 HETATM 6 C C5 FNM . . . Y 14 12.135 133.27 79.14 1 40.45 ? C5 FNM 2001 C 1 HETATM 7 C C6 FNM . . . Y 14 10.789 133.697 78.522 1 42.16 ? C6 FNM 2001 C 1 HETATM 8 O O6 FNM . . . Y 14 10.122 133.115 77.698 1 44.33 ? O6 FNM 2001 C 1 HETATM 9 C C7 FNM . . . Y 14 13.219 133.226 78.05 1 39.39 ? C7 FNM 2001 C 1 HETATM 10 C C8 FNM . . . Y 14 12.024 131.945 79.901 1 39.75 ? C8 FNM 2001 C 1 HETATM 11 C C9 FNM . . . Y 14 10.989 131.754 80.803 1 41.79 ? C9 FNM 2001 C 1 HETATM 12 C C10 FNM . . . Y 14 10.861 130.561 81.5 1 40.51 ? C10 FNM 2001 C 1 HETATM 13 C C11 FNM . . . Y 14 11.779 129.539 81.296 1 40.81 ? C11 FNM 2001 C 1 HETATM 14 C C12 FNM . . . Y 14 12.824 129.714 80.395 1 39.69 ? C12 FNM 2001 C 1 HETATM 15 C C13 FNM . . . Y 14 12.946 130.928 79.694 1 38.55 ? C13 FNM 2001 C 1 HETATM 16 C C21 FNM . . . Y 14 8.109 135.447 79.44 1 39.29 ? C21 FNM 2001 C 1 HETATM 17 C C22 FNM . . . Y 14 6.999 136.224 79.036 1 38.88 ? C22 FNM 2001 C 1 HETATM 18 C C23 FNM . . . Y 14 5.749 136.039 79.649 1 38.45 ? C23 FNM 2001 C 1 HETATM 19 C C24 FNM . . . Y 14 5.592 135.085 80.668 1 38.81 ? C24 FNM 2001 C 1 HETATM 20 C C25 FNM . . . Y 14 6.693 134.309 81.08 1 40.48 ? C25 FNM 2001 C 1 HETATM 21 C C26 FNM . . . Y 14 7.95 134.484 80.471 1 39.36 ? C26 FNM 2001 C 1 HETATM 22 C C27 FNM . . . Y 14 12.752 136.977 81.851 1 39.99 ? C27 FNM 2001 C 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #