data_6YMX # _model_server_result.job_id LL9u9Iqk9rMEuaMODnM8cw _model_server_result.datetime_utc '2024-12-27 03:31:22' _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 6ymx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"OA","auth_seq_id":302}' # _entry.id 6YMX # _exptl.entry_id 6YMX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 734.039 _entity.id 31 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE _entity.pdbx_number_of_molecules 5 _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 6YMX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YMX _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 PISA _pdbx_struct_assembly.oligomeric_details 32-meric _pdbx_struct_assembly.oligomeric_count 32 _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,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 _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 ? 31 OA N N ? 31 QA N N ? 31 UA N N ? 31 GB N N ? 31 RB 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 J SG CYS 22 j CYS 27 1_555 J SG CYS 54 j CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 J SG CYS 32 j CYS 37 1_555 J SG CYS 43 j CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 Q SG CYS 134 E CYS 164 1_555 Q SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 R SG CYS 28 F CYS 101 1_555 R SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 Z SG CYS 134 P CYS 164 1_555 Z SG CYS 150 P CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 AA SG CYS 29 Q CYS 101 1_555 AA SG CYS 51 Q CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 B N ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.287 ? covale ? covale2 B C ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.562 ? covale ? covale3 B CB ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.619 ? covale ? covale4 C CE MET 217 c MET 218 1_555 NA C36 PTY . c PTY 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale5 C CE MET 217 c MET 218 1_555 NA C37 PTY . c PTY 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A NE2 HIS 58 a HIS 62 1_555 HA FE HEA . a HEA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc2 A ND1 HIS 237 a HIS 241 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc3 A NE2 HIS 286 a HIS 290 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 A NE2 HIS 287 a HIS 291 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 A NE2 HIS 374 a HIS 378 1_555 HA FE HEA . a HEA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc6 B O GLU 208 b GLU 223 1_555 LA CU1 CUA . b CUA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc7 B ND1 HIS 214 b HIS 229 1_555 LA CU1 CUA . b CUA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc8 D SG CYS 105 d CYS 134 1_555 PA ZN ZN . d ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc9 O NE2 HIS 82 C HIS 82 1_555 WA FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc10 O NE2 HIS 96 C HIS 96 1_555 XA FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc11 O NE2 HIS 183 C HIS 183 1_555 WA FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc12 O NE2 HIS 197 C HIS 197 1_555 XA FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc13 P NE2 HIS 44 D HIS 105 1_555 CB FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc14 X NE2 HIS 82 N HIS 82 1_555 HB FE HEM . N HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc15 X NE2 HIS 96 N HIS 96 1_555 IB FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc16 X NE2 HIS 183 N HIS 183 1_555 HB FE HEM . N HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc17 X NE2 HIS 197 N HIS 197 1_555 IB FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc18 Y NE2 HIS 44 O HIS 105 1_555 OB FE HEM . O HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? # _chem_comp.formula 'C40 H80 N O8 P' _chem_comp.formula_weight 734.039 _chem_comp.id PCF _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6YMX _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 GA 26 CU a 1 601 601 CU CU . HA 27 HEA a 1 602 602 HEA HEA . IA 27 HEA a 1 603 603 HEA HEA . JA 28 PTY a 1 604 7 PTY PTY . KA 29 CN3 a 1 605 1 CN3 CN3 . LA 30 CUA b 1 301 301 CUA CUA . MA 28 PTY b 1 302 1 PTY PTY . NA 28 PTY c 1 301 6 PTY PTY . OA 31 PCF c 1 302 3 PCF PCF . PA 32 ZN d 1 201 1 ZN ZN . QA 31 PCF e 1 201 2 PCF PCF . RA 28 PTY i 1 101 3 PTY PTY . SA 28 PTY m 1 101 4 PTY PTY . TA 28 PTY m 1 102 5 PTY PTY . UA 31 PCF m 1 103 1 PCF PCF . VA 33 6PH C 1 401 401 6PH 6PH . WA 34 HEM C 1 402 402 HEM HEM . XA 34 HEM C 1 403 403 HEM HEM . YA 35 8PE C 1 404 404 8PE 8PE . ZA 36 CN5 C 1 405 405 CN5 CN5 . AB 37 UQ6 C 1 406 406 UQ6 UQ6 . BB 38 9PE C 1 407 401 9PE 9PE . CB 34 HEM D 1 401 401 HEM HEM . DB 28 PTY D 1 402 2 PTY PTY . EB 39 7PH E 1 301 402 7PH 7PH . FB 40 FES E 1 302 301 FES FES . GB 31 PCF I 1 101 101 PCF PCF . HB 34 HEM N 1 401 403 HEM HEM . IB 34 HEM N 1 402 404 HEM HEM . JB 37 UQ6 N 1 403 405 UQ6 UQ6 . KB 35 8PE N 1 404 406 8PE 8PE . LB 38 9PE N 1 405 407 9PE 9PE . MB 29 CN3 N 1 406 408 CN3 CN3 . NB 33 6PH O 1 401 402 6PH 6PH . OB 34 HEM O 1 402 401 HEM HEM . PB 39 7PH O 1 403 301 7PH 7PH . QB 40 FES P 1 301 302 FES FES . RB 31 PCF T 1 101 101 PCF PCF . # 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 N PCF . . . OA 31 217.72 199.731 104.915 1 216.81 ? N PCF 302 c 1 HETATM 2 P P PCF . . . OA 31 217.246 198.29 108.883 1 216.81 ? P PCF 302 c 1 HETATM 3 O O11 PCF . . . OA 31 216.531 197.45 110.091 1 216.81 ? O11 PCF 302 c 1 HETATM 4 O O12 PCF . . . OA 31 217.194 199.772 109.179 1 216.81 ? O12 PCF 302 c 1 HETATM 5 O O13 PCF . . . OA 31 216.22 198.036 107.639 1 216.81 ? O13 PCF 302 c 1 HETATM 6 O O14 PCF . . . OA 31 218.564 197.618 108.558 1 216.81 ? O14 PCF 302 c 1 HETATM 7 C C11 PCF . . . OA 31 216.128 199.073 106.681 1 216.81 ? C11 PCF 302 c 1 HETATM 8 C C12 PCF . . . OA 31 216.794 198.663 105.38 1 216.81 ? C12 PCF 302 c 1 HETATM 9 C C13 PCF . . . OA 31 218.89 199.884 105.896 1 216.81 ? C13 PCF 302 c 1 HETATM 10 C C14 PCF . . . OA 31 218.289 199.41 103.531 1 216.81 ? C14 PCF 302 c 1 HETATM 11 C C15 PCF . . . OA 31 217.02 201.084 104.754 1 216.81 ? C15 PCF 302 c 1 HETATM 12 C C1 PCF . . . OA 31 217.309 196.455 110.752 1 216.81 ? C1 PCF 302 c 1 HETATM 13 C C2 PCF . . . OA 31 216.605 195.911 111.99 1 216.81 ? C2 PCF 302 c 1 HETATM 14 C C3 PCF . . . OA 31 217.162 196.517 113.271 1 216.81 ? C3 PCF 302 c 1 HETATM 15 O O31 PCF . . . OA 31 216.982 195.574 114.331 1 216.81 ? O31 PCF 302 c 1 HETATM 16 O O32 PCF . . . OA 31 218.446 196.761 115.662 1 216.81 ? O32 PCF 302 c 1 HETATM 17 C C31 PCF . . . OA 31 217.706 195.806 115.463 1 216.81 ? C31 PCF 302 c 1 HETATM 18 C C32 PCF . . . OA 31 217.469 194.695 116.459 1 216.81 ? C32 PCF 302 c 1 HETATM 19 C C33 PCF . . . OA 31 215.987 194.393 116.676 1 216.81 ? C33 PCF 302 c 1 HETATM 20 C C34 PCF . . . OA 31 215.688 193.103 117.454 1 216.81 ? C34 PCF 302 c 1 HETATM 21 C C35 PCF . . . OA 31 214.211 192.908 117.804 1 216.81 ? C35 PCF 302 c 1 HETATM 22 C C36 PCF . . . OA 31 213.908 191.456 118.187 1 216.81 ? C36 PCF 302 c 1 HETATM 23 C C37 PCF . . . OA 31 214.229 191.098 119.644 1 216.81 ? C37 PCF 302 c 1 HETATM 24 C C38 PCF . . . OA 31 213.055 190.562 120.475 1 216.81 ? C38 PCF 302 c 1 HETATM 25 C C39 PCF . . . OA 31 213.468 189.74 121.7 1 216.81 ? C39 PCF 302 c 1 HETATM 26 C C40 PCF . . . OA 31 214.224 190.586 122.728 1 216.81 ? C40 PCF 302 c 1 HETATM 27 C C41 PCF . . . OA 31 214.558 189.77 123.98 1 216.81 ? C41 PCF 302 c 1 HETATM 28 C C42 PCF . . . OA 31 213.29 189.353 124.727 1 216.81 ? C42 PCF 302 c 1 HETATM 29 O O21 PCF . . . OA 31 215.211 196.215 111.918 1 216.81 ? O21 PCF 302 c 1 HETATM 30 O O22 PCF . . . OA 31 214.043 194.677 110.672 1 216.81 ? O22 PCF 302 c 1 HETATM 31 C C21 PCF . . . OA 31 214.4 195.133 111.747 1 216.81 ? C21 PCF 302 c 1 HETATM 32 C C22 PCF . . . OA 31 213.999 194.552 113.08 1 216.81 ? C22 PCF 302 c 1 HETATM 33 C C23 PCF . . . OA 31 213.748 193.047 112.985 1 216.81 ? C23 PCF 302 c 1 HETATM 34 C C24 PCF . . . OA 31 213.141 192.392 114.232 1 216.81 ? C24 PCF 302 c 1 HETATM 35 C C25 PCF . . . OA 31 211.629 192.585 114.376 1 216.81 ? C25 PCF 302 c 1 HETATM 36 C C26 PCF . . . OA 31 211.162 192.139 115.764 1 216.81 ? C26 PCF 302 c 1 HETATM 37 C C27 PCF . . . OA 31 209.643 192.151 115.97 1 216.81 ? C27 PCF 302 c 1 HETATM 38 C C28 PCF . . . OA 31 209.183 192.051 117.43 1 216.81 ? C28 PCF 302 c 1 HETATM 39 C C29 PCF . . . OA 31 207.822 191.386 117.631 1 216.81 ? C29 PCF 302 c 1 HETATM 40 C C30 PCF . . . OA 31 207.693 190.832 119.052 1 216.81 ? C30 PCF 302 c 1 HETATM 41 C C47 PCF . . . OA 31 208.734 189.747 119.349 1 216.81 ? C47 PCF 302 c 1 HETATM 42 C C48 PCF . . . OA 31 208.66 189.272 120.804 1 216.81 ? C48 PCF 302 c 1 HETATM 43 C C49 PCF . . . OA 31 209.294 187.898 121.047 1 216.81 ? C49 PCF 302 c 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 71 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #