data_5KLV # _model_server_result.job_id nOr-bmLM9JTR1rVwRe_mtw _model_server_result.datetime_utc '2024-11-05 06:50:08' _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 5klv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":1003}' # _entry.id 5KLV # _exptl.entry_id 5KLV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 311.401 _entity.id 16 _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 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 5KLV _cell.length_a 153.986 _cell.length_b 153.986 _cell.length_c 592.713 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KLV _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 22-meric _pdbx_struct_assembly.oligomeric_count 22 _pdbx_struct_assembly.details author_and_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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 153.986 153.986 0 # _struct_asym.details ? _struct_asym.entity_id 16 _struct_asym.id S _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 E SG CYS 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 H SG CYS 24 H CYS 24 1_555 H SG CYS 68 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 H SG CYS 40 H CYS 40 1_555 H SG CYS 54 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 D SG CYS 37 D CYS 37 1_555 V CAB HEC . D HEC 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? covale ? covale2 D SG CYS 40 D CYS 40 1_555 V CAC HEC . D HEC 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 Q FE HEM . C HEM 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 R FE HEM . C HEM 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 Q FE HEM . C HEM 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 R FE HEM . C HEM 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc5 D NE2 HIS 41 D HIS 41 1_555 V FE HEC . D HEC 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc6 D SD MET 160 D MET 160 1_555 V FE HEC . D HEC 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc7 E SG CYS 139 E CYS 139 1_555 Y FE1 FES . E FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc8 E ND1 HIS 141 E HIS 141 1_555 Y FE2 FES . E FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc9 E SG CYS 158 E CYS 158 1_555 Y FE1 FES . E FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc10 E ND1 HIS 161 E HIS 161 1_555 Y FE2 FES . E FES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? # _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 521 n n N1 C21 FNM sing 522 n n N2 C3 FNM sing 523 n n N2 C6 FNM sing 524 n n C3 S3 FNM sing 525 n n C3 N4 FNM doub 526 n n S3 C27 FNM sing 527 n n N4 C5 FNM sing 528 n n C5 C6 FNM sing 529 n n C5 C7 FNM sing 530 n n C5 C8 FNM sing 531 n n C6 O6 FNM doub 532 n n C8 C9 FNM doub 533 n y C8 C13 FNM sing 534 n y C9 C10 FNM sing 535 n y C10 C11 FNM doub 536 n y C11 C12 FNM sing 537 n y C12 C13 FNM doub 538 n y C21 C22 FNM doub 539 n y C21 C26 FNM sing 540 n y C22 C23 FNM sing 541 n y C23 C24 FNM doub 542 n y C24 C25 FNM sing 543 n y C25 C26 FNM doub 544 n y N1 HN1 FNM sing 545 n n C7 H7 FNM sing 546 n n C7 H7A FNM sing 547 n n C7 H7B FNM sing 548 n n C9 H9 FNM sing 549 n n C10 H10 FNM sing 550 n n C11 H11 FNM sing 551 n n C12 H12 FNM sing 552 n n C13 H13 FNM sing 553 n n C22 H22 FNM sing 554 n n C23 H23 FNM sing 555 n n C24 H24 FNM sing 556 n n C25 H25 FNM sing 557 n n C26 H26 FNM sing 558 n n C27 H27 FNM sing 559 n n C27 H27A FNM sing 560 n n C27 H27B FNM sing 561 n n # _atom_sites.entry_id 5KLV _atom_sites.fract_transf_matrix[1][1] 0.006494 _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] 0.006494 _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] 0.001687 _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 L 12 6PE A 1 501 2 6PE 6PE . M 13 CDL A 1 502 8 CDL CDL . N 14 GOL B 1 501 1 GOL GOL . O 14 GOL B 1 502 2 GOL GOL . P 14 GOL B 1 503 3 GOL GOL . Q 15 HEM C 1 1001 1001 HEM HEM . R 15 HEM C 1 1002 1002 HEM HEM . S 16 FNM C 1 1003 1101 FNM FNM . T 17 8PE C 1 1004 3 8PE 8PE . U 18 CL C 1 1005 4 CL CL . V 19 HEC D 1 1001 1001 HEC HEC . W 20 PEF D 1 1002 4 PEF PEF . X 13 CDL D 1 1003 7 CDL CDL . Y 21 FES E 1 1001 1001 FES FES . Z 13 CDL G 1 101 6 CDL CDL . AA 22 PX4 J 1 101 5 PX4 PX4 . BA 12 6PE K 1 101 1 6PE 6PE . CA 23 HOH A 1 601 6 HOH HOH . CA 23 HOH A 2 602 5 HOH HOH . CA 23 HOH A 3 603 48 HOH HOH . CA 23 HOH A 4 604 3 HOH HOH . CA 23 HOH A 5 605 2 HOH HOH . CA 23 HOH A 6 606 4 HOH HOH . CA 23 HOH A 7 607 1 HOH HOH . CA 23 HOH A 8 608 7 HOH HOH . DA 23 HOH B 1 601 33 HOH HOH . DA 23 HOH B 2 602 21 HOH HOH . DA 23 HOH B 3 603 10 HOH HOH . DA 23 HOH B 4 604 29 HOH HOH . DA 23 HOH B 5 605 13 HOH HOH . DA 23 HOH B 6 606 8 HOH HOH . DA 23 HOH B 7 607 9 HOH HOH . DA 23 HOH B 8 608 20 HOH HOH . DA 23 HOH B 9 609 17 HOH HOH . DA 23 HOH B 10 610 19 HOH HOH . DA 23 HOH B 11 611 18 HOH HOH . DA 23 HOH B 12 612 11 HOH HOH . DA 23 HOH B 13 613 31 HOH HOH . DA 23 HOH B 14 614 35 HOH HOH . DA 23 HOH B 15 615 22 HOH HOH . DA 23 HOH B 16 616 24 HOH HOH . DA 23 HOH B 17 617 15 HOH HOH . DA 23 HOH B 18 618 25 HOH HOH . DA 23 HOH B 19 619 27 HOH HOH . DA 23 HOH B 20 620 12 HOH HOH . DA 23 HOH B 21 621 16 HOH HOH . DA 23 HOH B 22 622 26 HOH HOH . DA 23 HOH B 23 623 23 HOH HOH . DA 23 HOH B 24 624 30 HOH HOH . DA 23 HOH B 25 625 28 HOH HOH . DA 23 HOH B 26 626 14 HOH HOH . DA 23 HOH B 27 627 32 HOH HOH . DA 23 HOH B 28 628 34 HOH HOH . EA 23 HOH C 1 1101 38 HOH HOH . EA 23 HOH C 2 1102 36 HOH HOH . EA 23 HOH C 3 1103 1102 HOH HOH . EA 23 HOH C 4 1104 37 HOH HOH . FA 23 HOH D 1 1101 40 HOH HOH . FA 23 HOH D 2 1102 39 HOH HOH . FA 23 HOH D 3 1103 42 HOH HOH . FA 23 HOH D 4 1104 41 HOH HOH . GA 23 HOH F 1 201 47 HOH HOH . GA 23 HOH F 2 202 46 HOH HOH . GA 23 HOH F 3 203 44 HOH HOH . GA 23 HOH F 4 204 43 HOH HOH . GA 23 HOH F 5 205 45 HOH HOH . HA 23 HOH I 1 101 49 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 . . . S 16 67.852 57.334 170.282 1 86.91 ? N1 FNM 1003 C 1 HETATM 2 N N2 FNM . . . S 16 68.213 58.21 169.243 1 85.26 ? N2 FNM 1003 C 1 HETATM 3 C C3 FNM . . . S 16 69.194 59.184 169.38 1 84.11 ? C3 FNM 1003 C 1 HETATM 4 S S3 FNM . . . S 16 69.998 59.309 170.978 1 84.29 ? S3 FNM 1003 C 1 HETATM 5 N N4 FNM . . . S 16 69.406 59.884 168.353 1 82.38 ? N4 FNM 1003 C 1 HETATM 6 C C5 FNM . . . S 16 68.47 59.398 167.291 1 82.54 ? C5 FNM 1003 C 1 HETATM 7 C C6 FNM . . . S 16 67.702 58.259 167.969 1 83.6 ? C6 FNM 1003 C 1 HETATM 8 O O6 FNM . . . S 16 66.83 57.55 167.522 1 83.16 ? O6 FNM 1003 C 1 HETATM 9 C C7 FNM . . . S 16 67.457 60.518 167.004 1 82.07 ? C7 FNM 1003 C 1 HETATM 10 C C8 FNM . . . S 16 69.222 58.918 166.05 1 82.43 ? C8 FNM 1003 C 1 HETATM 11 C C9 FNM . . . S 16 70.032 57.796 166.158 1 83.46 ? C9 FNM 1003 C 1 HETATM 12 C C10 FNM . . . S 16 70.732 57.324 165.059 1 82.2 ? C10 FNM 1003 C 1 HETATM 13 C C11 FNM . . . S 16 70.634 57.966 163.84 1 79.95 ? C11 FNM 1003 C 1 HETATM 14 C C12 FNM . . . S 16 69.828 59.083 163.725 1 79.41 ? C12 FNM 1003 C 1 HETATM 15 C C13 FNM . . . S 16 69.125 59.56 164.816 1 80.45 ? C13 FNM 1003 C 1 HETATM 16 C C21 FNM . . . S 16 68.498 56.043 170.434 1 87.71 ? C21 FNM 1003 C 1 HETATM 17 C C22 FNM . . . S 16 69.585 55.751 169.629 1 87.18 ? C22 FNM 1003 C 1 HETATM 18 C C23 FNM . . . S 16 70.222 54.528 169.747 1 88.44 ? C23 FNM 1003 C 1 HETATM 19 C C24 FNM . . . S 16 69.776 53.597 170.671 1 90.11 ? C24 FNM 1003 C 1 HETATM 20 C C25 FNM . . . S 16 68.686 53.892 171.472 1 90.26 ? C25 FNM 1003 C 1 HETATM 21 C C26 FNM . . . S 16 68.047 55.114 171.354 1 89.07 ? C26 FNM 1003 C 1 HETATM 22 C C27 FNM . . . S 16 71.699 59.759 170.314 1 84.5 ? C27 FNM 1003 C 1 HETATM 23 H HN1 FNM . . . S 16 67.13 57.644 170.909 1 104.51 ? HN1 FNM 1003 C 1 HETATM 24 H H7 FNM . . . S 16 66.759 60.192 166.245 1 98.7 ? H7 FNM 1003 C 1 HETATM 25 H H7A FNM . . . S 16 67.995 61.387 166.652 1 98.7 ? H7A FNM 1003 C 1 HETATM 26 H H7B FNM . . . S 16 66.915 60.778 167.905 1 98.7 ? H7B FNM 1003 C 1 HETATM 27 H H9 FNM . . . S 16 70.107 57.302 167.103 1 100.37 ? H9 FNM 1003 C 1 HETATM 28 H H10 FNM . . . S 16 71.354 56.456 165.16 1 98.86 ? H10 FNM 1003 C 1 HETATM 29 H H11 FNM . . . S 16 71.175 57.6 162.99 1 96.17 ? H11 FNM 1003 C 1 HETATM 30 H H12 FNM . . . S 16 69.743 59.588 162.783 1 95.51 ? H12 FNM 1003 C 1 HETATM 31 H H13 FNM . . . S 16 68.504 60.426 164.721 1 96.76 ? H13 FNM 1003 C 1 HETATM 32 H H22 FNM . . . S 16 69.917 56.483 168.923 1 104.84 ? H22 FNM 1003 C 1 HETATM 33 H H23 FNM . . . S 16 71.065 54.305 169.124 1 106.35 ? H23 FNM 1003 C 1 HETATM 34 H H24 FNM . . . S 16 70.269 52.649 170.762 1 108.36 ? H24 FNM 1003 C 1 HETATM 35 H H25 FNM . . . S 16 68.334 53.176 172.188 1 108.53 ? H25 FNM 1003 C 1 HETATM 36 H H26 FNM . . . S 16 67.205 55.357 171.968 1 107.1 ? H26 FNM 1003 C 1 HETATM 37 H H27 FNM . . . S 16 72.348 59.977 171.145 1 101.62 ? H27 FNM 1003 C 1 HETATM 38 H H27A FNM . . . S 16 71.546 60.628 169.695 1 101.62 ? H27A FNM 1003 C 1 HETATM 39 H H27B FNM . . . S 16 72.079 58.929 169.745 1 101.62 ? H27B FNM 1003 C 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 362 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #