data_7YML # _model_server_result.job_id Jwhhf5otYGbUjKwM_nwNEQ _model_server_result.datetime_utc '2025-02-26 08:14:03' _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 7yml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":305}' # _entry.id 7YML # _exptl.entry_id 7YML _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 749.007 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE' _entity.pdbx_number_of_molecules 8 _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 7YML _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YML _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 24-meric _pdbx_struct_assembly.oligomeric_count 24 _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,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC,MC,NC,OC,PC,QC,RC,SC,TC,UC,VC,WC,XC,YC,ZC,AD,BD,CD,DD,ED,FD,GD,HD,ID,JD,KD _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 ? 10 CA N N ? 10 KA N N ? 10 VA N N ? 10 WA N N ? 10 XA N N ? 10 FB N N ? 10 GB N N ? 10 OC 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 covale ? covale1 D C FME 1 A FME 1 1_555 D N SER 2 A SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 F C FME 1 D FME 1 1_555 F N SER 2 D SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 H C FME 1 F FME 1 1_555 H N SER 2 F SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 J C FME 1 I FME 1 1_555 J N SER 2 I SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 L C FME 1 K FME 1 1_555 L N SER 2 K SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 N C FME 1 O FME 1 1_555 N N SER 2 O SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 P C FME 1 Q FME 1 1_555 P N SER 2 Q SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 R C FME 1 S FME 1 1_555 R N SER 2 S SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 T C FME 1 V FME 1 1_555 T N SER 2 V SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A NE2 HIS 191 L HIS 191 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc2 A NE2 HIS 231 L HIS 231 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc3 B NE2 HIS 218 M HIS 218 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc4 B OE1 GLU 233 M GLU 233 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc5 B OE2 GLU 233 M GLU 233 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc6 B NE2 HIS 265 M HIS 265 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc7 RB MG BCL . F BCL 101 1_555 SB O1 MYR . F MYR 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? # _chem_comp.formula 'C40 H77 O10 P' _chem_comp.formula_weight 749.007 _chem_comp.id PGV _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PHOSPHATIDYLGLYCEROL;2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL # _atom_sites.entry_id 7YML _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 Y 7 BCL L 1 301 301 BCL BCL . Z 8 BPH L 1 302 302 BPH BPH . AA 9 U10 L 1 303 310 U10 U10 . BA 9 U10 L 1 304 312 U10 U10 . CA 10 PGV L 1 305 316 PGV PGV . DA 11 PEE L 1 306 317 PEE PEE . EA 12 LDA L 1 307 318 LDA LDA . FA 13 LMT L 1 308 319 LMT LMT . GA 13 LMT L 1 309 320 LMT LMT . HA 7 BCL L 1 310 401 BCL BCL . IA 13 LMT L 1 311 307 LMT LMT . JA 9 U10 M 1 401 311 U10 U10 . KA 10 PGV M 1 402 315 PGV PGV . LA 7 BCL M 1 403 402 BCL BCL . MA 7 BCL M 1 404 403 BCL BCL . NA 8 BPH M 1 405 404 BPH BPH . OA 14 FE M 1 406 410 FE FE . PA 9 U10 M 1 407 411 U10 U10 . QA 15 SPO M 1 408 412 SPO SPO . RA 13 LMT M 1 409 418 LMT LMT . SA 13 LMT M 1 410 420 LMT LMT . TA 13 LMT M 1 411 422 LMT LMT . UA 13 LMT M 1 412 423 LMT LMT . VA 10 PGV M 1 413 424 PGV PGV . WA 10 PGV M 1 414 425 PGV PGV . XA 10 PGV M 1 415 426 PGV PGV . YA 12 LDA M 1 416 428 LDA LDA . ZA 13 LMT M 1 417 429 LMT LMT . AB 12 LDA M 1 418 430 LDA LDA . BB 12 LDA M 1 419 431 LDA LDA . CB 12 LDA M 1 420 433 LDA LDA . DB 12 LDA H 1 301 413 LDA LDA . EB 12 LDA H 1 302 416 LDA LDA . FB 10 PGV H 1 303 305 PGV PGV . GB 10 PGV H 1 304 306 PGV PGV . HB 7 BCL A 1 101 101 BCL BCL . IB 13 LMT A 1 102 201 LMT LMT . JB 7 BCL B 1 101 101 BCL BCL . KB 15 SPO D 1 101 110 SPO SPO . LB 7 BCL D 1 102 101 BCL BCL . MB 15 SPO D 1 103 110 SPO SPO . NB 12 LDA D 1 104 112 LDA LDA . OB 15 SPO D 1 105 110 SPO SPO . PB 15 SPO E 1 101 111 SPO SPO . QB 7 BCL E 1 102 101 BCL BCL . RB 7 BCL F 1 101 310 BCL BCL . SB 16 MYR F 1 102 311 MYR MYR . TB 7 BCL F 1 103 101 BCL BCL . UB 15 SPO F 1 104 111 SPO SPO . VB 7 BCL G 1 101 101 BCL BCL . WB 15 SPO G 1 102 111 SPO SPO . XB 13 LMT I 1 101 314 LMT LMT . YB 7 BCL I 1 102 101 BCL BCL . ZB 15 SPO I 1 103 110 SPO SPO . AC 15 SPO I 1 104 110 SPO SPO . BC 7 BCL J 1 101 101 BCL BCL . CC 13 LMT K 1 101 302 LMT LMT . DC 7 BCL K 1 102 101 BCL BCL . EC 15 SPO N 1 101 111 SPO SPO . FC 7 BCL N 1 102 101 BCL BCL . GC 12 LDA O 1 101 435 LDA LDA . HC 7 BCL O 1 102 101 BCL BCL . IC 15 SPO O 1 103 110 SPO SPO . JC 15 SPO O 1 104 110 SPO SPO . KC 15 SPO P 1 101 111 SPO SPO . LC 7 BCL P 1 102 101 BCL BCL . MC 13 LMT Q 1 101 414 LMT LMT . NC 12 LDA Q 1 102 417 LDA LDA . OC 10 PGV Q 1 103 427 PGV PGV . PC 12 LDA Q 1 104 434 LDA LDA . QC 7 BCL Q 1 105 101 BCL BCL . RC 15 SPO R 1 101 111 SPO SPO . SC 7 BCL R 1 102 101 BCL BCL . TC 13 LMT S 1 101 415 LMT LMT . UC 13 LMT S 1 102 419 LMT LMT . VC 7 BCL S 1 103 101 BCL BCL . WC 15 SPO S 1 104 110 SPO SPO . XC 15 SPO S 1 105 110 SPO SPO . YC 15 SPO T 1 101 111 SPO SPO . ZC 7 BCL T 1 102 101 BCL BCL . AD 7 BCL V 1 101 101 BCL BCL . BD 15 SPO W 1 101 111 SPO SPO . CD 7 BCL W 1 102 101 BCL BCL . DD 13 LMT Y 1 101 421 LMT LMT . ED 7 BCL Y 1 102 101 BCL BCL . FD 13 LMT Y 1 103 432 LMT LMT . GD 7 BCL Z 1 101 101 BCL BCL . HD 13 LMT X 1 101 321 LMT LMT . ID 13 LMT X 1 102 301 LMT LMT . JD 17 HOH L 1 401 1 HOH HOH . JD 17 HOH L 2 402 3 HOH HOH . JD 17 HOH L 3 403 4 HOH HOH . JD 17 HOH L 4 404 2 HOH HOH . KD 17 HOH M 1 501 6 HOH HOH . KD 17 HOH M 2 502 5 HOH HOH . KD 17 HOH M 3 503 7 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 P P PGV . . . CA 10 187.879 164.778 160.08 1 107.2 ? P PGV 305 L 1 HETATM 2 C C01 PGV . . . CA 10 184.183 165.836 160.728 1 93.68 ? C01 PGV 305 L 1 HETATM 3 C C02 PGV . . . CA 10 184.888 166.091 162.057 1 91.61 ? C02 PGV 305 L 1 HETATM 4 C C03 PGV . . . CA 10 186.215 165.346 162.034 1 86.58 ? C03 PGV 305 L 1 HETATM 5 C C04 PGV . . . CA 10 188.762 163.665 157.884 1 91.63 ? C04 PGV 305 L 1 HETATM 6 C C05 PGV . . . CA 10 188.325 162.923 156.629 1 92.78 ? C05 PGV 305 L 1 HETATM 7 C C06 PGV . . . CA 10 189.56 162.59 155.8 1 91.94 ? C06 PGV 305 L 1 HETATM 8 O O01 PGV . . . CA 10 184.061 165.64 163.129 1 93.5 ? O01 PGV 305 L 1 HETATM 9 O O02 PGV . . . CA 10 185.424 166.43 164.816 1 91.53 ? O02 PGV 305 L 1 HETATM 10 O O03 PGV . . . CA 10 182.776 166.004 160.887 1 98.16 ? O03 PGV 305 L 1 HETATM 11 O O04 PGV . . . CA 10 182.255 164.611 159.115 1 87.76 ? O04 PGV 305 L 1 HETATM 12 O O05 PGV . . . CA 10 187.45 163.758 155.865 1 92.3 ? O05 PGV 305 L 1 HETATM 13 O O06 PGV . . . CA 10 190.244 163.796 155.442 1 91.55 ? O06 PGV 305 L 1 HETATM 14 O O11 PGV . . . CA 10 186.412 164.815 160.729 1 89.69 ? O11 PGV 305 L 1 HETATM 15 O O12 PGV . . . CA 10 187.638 164.001 158.692 1 93.21 ? O12 PGV 305 L 1 HETATM 16 O O13 PGV . . . CA 10 188.774 163.93 160.945 1 95.96 ? O13 PGV 305 L 1 HETATM 17 O O14 PGV . . . CA 10 188.295 166.195 159.774 1 98.15 ? O14 PGV 305 L 1 HETATM 18 C C1 PGV . . . CA 10 184.294 166.343 164.379 1 91.25 ? C1 PGV 305 L 1 HETATM 19 C C2 PGV . . . CA 10 183.142 166.941 165.147 1 91.37 ? C2 PGV 305 L 1 HETATM 20 C C3 PGV . . . CA 10 182.42 165.86 165.942 1 91.37 ? C3 PGV 305 L 1 HETATM 21 C C4 PGV . . . CA 10 181.242 166.467 166.693 1 92.18 ? C4 PGV 305 L 1 HETATM 22 C C5 PGV . . . CA 10 180.275 167.128 165.716 1 95.15 ? C5 PGV 305 L 1 HETATM 23 C C6 PGV . . . CA 10 179.458 168.235 166.37 1 94.02 ? C6 PGV 305 L 1 HETATM 24 C C7 PGV . . . CA 10 180.297 169.496 166.53 1 91.91 ? C7 PGV 305 L 1 HETATM 25 C C8 PGV . . . CA 10 180.619 169.758 167.994 1 91.71 ? C8 PGV 305 L 1 HETATM 26 C C9 PGV . . . CA 10 179.367 170.16 168.759 1 90.8 ? C9 PGV 305 L 1 HETATM 27 C C10 PGV . . . CA 10 179.251 169.342 170.036 1 91.43 ? C10 PGV 305 L 1 HETATM 28 C C11 PGV . . . CA 10 180.521 169.499 170.831 1 91.3 ? C11 PGV 305 L 1 HETATM 29 C C12 PGV . . . CA 10 180.462 169.648 172.148 1 89.72 ? C12 PGV 305 L 1 HETATM 30 C C19 PGV . . . CA 10 181.851 165.203 160.101 1 93.07 ? C19 PGV 305 L 1 HETATM 31 C C20 PGV . . . CA 10 180.408 165.1 160.523 1 90.76 ? C20 PGV 305 L 1 HETATM 32 C C21 PGV . . . CA 10 180.333 164.806 162.017 1 88.3 ? C21 PGV 305 L 1 HETATM 33 C C22 PGV . . . CA 10 178.904 164.454 162.401 1 90.28 ? C22 PGV 305 L 1 HETATM 34 C C23 PGV . . . CA 10 178.655 164.57 163.898 1 92.16 ? C23 PGV 305 L 1 HETATM 35 C C24 PGV . . . CA 10 179.188 163.369 164.669 1 92.49 ? C24 PGV 305 L 1 HETATM 36 C C25 PGV . . . CA 10 178.346 163.091 165.909 1 90.45 ? C25 PGV 305 L 1 HETATM 37 C C26 PGV . . . CA 10 178.065 164.368 166.693 1 93.53 ? C26 PGV 305 L 1 HETATM 38 C C27 PGV . . . CA 10 176.564 164.594 166.847 1 92.32 ? C27 PGV 305 L 1 HETATM 39 C C28 PGV . . . CA 10 176.272 165.915 167.551 1 87.9 ? C28 PGV 305 L 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #