data_5XTD # _model_server_result.job_id pdN3OeFL3x0L7qTSd-nkhg _model_server_result.datetime_utc '2024-10-31 07:18:23' _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 5xtd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"WB","auth_seq_id":502}' # _entry.id 5XTD # _exptl.entry_id 5XTD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 767.132 _entity.id 47 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL _entity.pdbx_number_of_molecules 9 _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 5XTD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XTD _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 ? _pdbx_struct_assembly.oligomeric_details 45-meric _pdbx_struct_assembly.oligomeric_count 45 _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,OB,PB,QB,RB,SB,TB,UB,VB,WB _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 47 XA N N ? 47 FB N N ? 47 IB N N ? 47 KB N N ? 47 LB N N ? 47 MB N N ? 47 NB N N ? 47 VB N N ? 47 WB 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 T SG CYS 94 V CYS 95 1_555 T SG CYS 114 V CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 AA SG CYS 111 c CYS 144 1_555 JA SG CYS 279 l CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf3 BA SG CYS 149 d CYS 149 1_555 CA SG CYS 88 e CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 FA SG CYS 32 h CYS 33 1_555 FA SG CYS 65 h CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 FA SG CYS 42 h CYS 43 1_555 FA SG CYS 55 h CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 QA SG CYS 75 u CYS 78 1_555 QA SG CYS 107 u CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf7 RA SG CYS 69 v CYS 69 1_555 RA SG CYS 80 v CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc1 A NE2 GLN 355 A GLN 381 1_555 TA FE1 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc2 B N CYS 80 B CYS 114 1_555 VA FE2 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc3 B N GLY 120 B GLY 154 1_555 WA FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc4 C SG CYS 32 C CYS 89 1_555 YA FE2 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc5 L NE2 HIS 95 M HIS 124 1_555 BB FE3 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc6 L SG CYS 108 M CYS 137 1_555 BB FE4 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? covale ? covale1 L SG CYS 147 M CYS 176 1_555 CB S3 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc7 L SG CYS 147 M CYS 176 1_555 CB FE1 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc8 L O CYS 150 M CYS 179 1_555 CB FE1 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc9 N SG CYS 141 O CYS 176 1_555 EB FE2 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc10 N SG CYS 145 O CYS 180 1_555 EB FE2 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? # _chem_comp.formula 'C42 H89 N O8 P 1' _chem_comp.formula_weight 767.132 _chem_comp.id PLX _chem_comp.mon_nstd_flag . _chem_comp.name (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5XTD _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 TA 45 SF4 A 1 501 501 SF4 SF4 . UA 46 FMN A 1 502 502 FMN FMN . VA 45 SF4 B 1 301 301 SF4 SF4 . WA 45 SF4 B 1 302 302 SF4 SF4 . XA 47 PLX B 1 303 401 PLX PLX . YA 45 SF4 C 1 301 301 SF4 SF4 . ZA 48 8Q1 E 1 201 201 8Q1 8Q1 . AB 49 NDP J 1 401 401 NDP NDP . BB 45 SF4 M 1 801 801 SF4 SF4 . CB 45 SF4 M 1 802 802 SF4 SF4 . DB 50 FES M 1 803 803 FES FES . EB 50 FES O 1 301 301 FES FES . FB 47 PLX U 1 101 101 PLX PLX . GB 51 CDL V 1 201 201 CDL CDL . HB 52 PEE V 1 202 202 PEE PEE . IB 47 PLX V 1 203 203 PLX PLX . JB 52 PEE W 1 201 201 PEE PEE . KB 47 PLX b 1 201 201 PLX PLX . LB 47 PLX g 1 201 201 PLX PLX . MB 47 PLX g 1 202 202 PLX PLX . NB 47 PLX g 1 203 203 PLX PLX . OB 51 CDL i 1 401 401 CDL CDL . PB 52 PEE l 1 701 701 PEE PEE . QB 52 PEE l 1 702 702 PEE PEE . RB 51 CDL l 1 703 703 CDL CDL . SB 51 CDL l 1 704 704 CDL CDL . TB 51 CDL n 1 101 101 CDL CDL . UB 48 8Q1 p 1 201 201 8Q1 8Q1 . VB 47 PLX r 1 501 501 PLX PLX . WB 47 PLX r 1 502 502 PLX PLX . # 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 C23 PLX . . . WB 47 335.546 247.691 234.517 1 40.69 ? C23 PLX 502 r 1 HETATM 2 C C22 PLX . . . WB 47 335.161 249.03 235.108 1 41.04 ? C22 PLX 502 r 1 HETATM 3 C C21 PLX . . . WB 47 333.856 249.547 234.512 1 40.14 ? C21 PLX 502 r 1 HETATM 4 C C20 PLX . . . WB 47 333.634 248.982 233.116 1 40.19 ? C20 PLX 502 r 1 HETATM 5 C C19 PLX . . . WB 47 332.646 249.827 232.324 1 37.39 ? C19 PLX 502 r 1 HETATM 6 C C18 PLX . . . WB 47 332.29 249.139 231.014 1 33.56 ? C18 PLX 502 r 1 HETATM 7 C C17 PLX . . . WB 47 330.793 249.205 230.729 1 31.18 ? C17 PLX 502 r 1 HETATM 8 C C16 PLX . . . WB 47 329.987 249.507 231.988 1 31.66 ? C16 PLX 502 r 1 HETATM 9 C C15 PLX . . . WB 47 328.739 248.633 232.076 1 33.01 ? C15 PLX 502 r 1 HETATM 10 C C14 PLX . . . WB 47 327.46 249.463 232.07 1 32.58 ? C14 PLX 502 r 1 HETATM 11 C C13 PLX . . . WB 47 326.268 248.619 231.641 1 31.76 ? C13 PLX 502 r 1 HETATM 12 C C12 PLX . . . WB 47 326.48 247.156 232.008 1 32.14 ? C12 PLX 502 r 1 HETATM 13 C C11 PLX . . . WB 47 326.484 246.267 230.77 1 32.89 ? C11 PLX 502 r 1 HETATM 14 C C10 PLX . . . WB 47 325.362 245.235 230.83 1 33.8 ? C10 PLX 502 r 1 HETATM 15 C C9 PLX . . . WB 47 324.43 245.358 229.628 1 35.24 ? C9 PLX 502 r 1 HETATM 16 C C8 PLX . . . WB 47 323.001 244.942 229.957 1 36.45 ? C8 PLX 502 r 1 HETATM 17 C C7 PLX . . . WB 47 322.456 244.009 228.884 1 37.52 ? C7 PLX 502 r 1 HETATM 18 C C6 PLX . . . WB 47 323.347 242.784 228.733 1 36.56 ? C6 PLX 502 r 1 HETATM 19 O O7 PLX . . . WB 47 323.828 242.374 230.017 1 37.4 ? O7 PLX 502 r 1 HETATM 20 O O6 PLX . . . WB 47 322.639 241.704 228.126 1 33.47 ? O6 PLX 502 r 1 HETATM 21 C C4 PLX . . . WB 47 321.266 241.618 228.5 1 30.66 ? C4 PLX 502 r 1 HETATM 22 C C3 PLX . . . WB 47 320.435 242.461 227.546 1 27.81 ? C3 PLX 502 r 1 HETATM 23 O O4 PLX . . . WB 47 320.824 242.217 226.2 1 22.36 ? O4 PLX 502 r 1 HETATM 24 P P1 PLX . . . WB 47 320.038 241.135 225.316 1 19.23 ? P1 PLX 502 r 1 HETATM 25 O O1 PLX . . . WB 47 321.228 240.22 224.751 1 14.54 ? O1 PLX 502 r 1 HETATM 26 C C2 PLX . . . WB 47 321.539 240.238 223.362 1 9.09 ? C2 PLX 502 r 1 HETATM 27 C C1 PLX . . . WB 47 322.911 239.619 223.156 1 2.37 ? C1 PLX 502 r 1 HETATM 28 N N1 PLX . . . WB 47 322.889 238.822 221.929 1 2.22 ? N1 PLX 502 r 1 HETATM 29 C C1C PLX . . . WB 47 324.098 237.998 221.88 1 2 ? C1C PLX 502 r 1 HETATM 30 C C1B PLX . . . WB 47 321.704 237.959 221.925 1 2.26 ? C1B PLX 502 r 1 HETATM 31 C C1A PLX . . . WB 47 322.848 239.706 220.76 1 2 ? C1A PLX 502 r 1 HETATM 32 O O2 PLX . . . WB 47 319.398 241.839 224.147 1 19.56 ? O2 PLX 502 r 1 HETATM 33 C C5 PLX . . . WB 47 320.81 240.169 228.414 1 33.4 ? C5 PLX 502 r 1 HETATM 34 O O8 PLX . . . WB 47 319.819 239.896 229.404 1 37.15 ? O8 PLX 502 r 1 HETATM 35 C C24 PLX . . . WB 47 319.608 238.495 229.56 1 38.76 ? C24 PLX 502 r 1 HETATM 36 O O9 PLX . . . WB 47 319.313 237.929 228.279 1 38.8 ? O9 PLX 502 r 1 HETATM 37 C C25 PLX . . . WB 47 318.485 238.238 230.564 1 38.96 ? C25 PLX 502 r 1 HETATM 38 C C26 PLX . . . WB 47 317.199 237.718 229.933 1 38.45 ? C26 PLX 502 r 1 HETATM 39 C C27 PLX . . . WB 47 316.922 236.289 230.37 1 37.88 ? C27 PLX 502 r 1 HETATM 40 C C28 PLX . . . WB 47 315.863 236.252 231.461 1 37.56 ? C28 PLX 502 r 1 HETATM 41 C C29 PLX . . . WB 47 314.754 235.272 231.108 1 40.01 ? C29 PLX 502 r 1 HETATM 42 C C30 PLX . . . WB 47 314.26 234.549 232.35 1 42.17 ? C30 PLX 502 r 1 HETATM 43 C C31 PLX . . . WB 47 315.432 233.945 233.105 1 43.78 ? C31 PLX 502 r 1 HETATM 44 C C32 PLX . . . WB 47 314.972 233.127 234.301 1 45.48 ? C32 PLX 502 r 1 HETATM 45 C C33 PLX . . . WB 47 313.559 232.612 234.094 1 46.77 ? C33 PLX 502 r 1 HETATM 46 C C34 PLX . . . WB 47 313.199 231.563 235.138 1 48 ? C34 PLX 502 r 1 HETATM 47 C C35 PLX . . . WB 47 312.301 232.144 236.222 1 46.66 ? C35 PLX 502 r 1 HETATM 48 C C36 PLX . . . WB 47 310.846 232.211 235.772 1 44.97 ? C36 PLX 502 r 1 HETATM 49 C C37 PLX . . . WB 47 310.728 232.83 234.386 1 42.83 ? C37 PLX 502 r 1 HETATM 50 C C38 PLX . . . WB 47 309.611 233.862 234.323 1 40.79 ? C38 PLX 502 r 1 HETATM 51 C C39 PLX . . . WB 47 308.557 233.581 235.366 1 38.57 ? C39 PLX 502 r 1 HETATM 52 O O3 PLX . . . WB 47 319.202 240.3 226.248 1 15.39 ? O3 PLX 502 r 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 84 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 52 #