data_6RQF
#
_model_server_result.job_id            SxGgHpbF1VlP-PXiE3EF7w 
_model_server_result.datetime_utc      '2025-03-06 09:16:30' 
_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          6rqf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Y","auth_seq_id":202}' 
#
_entry.id    6RQF 
#
_exptl.entry_id    6RQF 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              749.007 
_entity.id                          16 
_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    4 
_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            6RQF 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6RQF 
_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    hexadecameric 
_pdbx_struct_assembly.oligomeric_count      16 
_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 
_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
? 16 Y N N 
? 16 AA N N 
? 16 LA N N 
? 16 MA 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 D SG CYS 112 L CYS 112 1_555 D SG CYS 127 L CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
disulf ? disulf2 L SG CYS 112 D CYS 112 1_555 L SG CYS 127 D CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
covale ? covale1 A SG CYS 35 I CYS 35 1_555 S CAB HEC . I HEC 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.76 ? 
metalc ? metalc1 A NE2 HIS 86 I HIS 86 1_555 Q FE HEM . I HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? 
metalc ? metalc2 A NE2 HIS 100 I HIS 100 1_555 R FE HEM . I HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? 
metalc ? metalc3 A NE2 HIS 187 I HIS 187 1_555 Q FE HEM . I HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? 
metalc ? metalc4 A NE2 HIS 202 I HIS 202 1_555 R FE HEM . I HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? 
metalc ? metalc5 C N TYR 1 K TYR 1 1_555 Z FE HEC . K HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
covale ? covale2 C SG CYS 21 K CYS 21 1_555 Z CBB HEC . K HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? 
covale ? covale3 C SG CYS 21 K CYS 21 1_555 Z CAB HEC . K HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? 
covale ? covale4 C SG CYS 24 K CYS 24 1_555 Z CBC HEC . K HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? 
metalc ? metalc6 D SG CYS 107 L CYS 107 1_555 BA FE1 FES . L FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc7 D ND1 HIS 109 L HIS 109 1_555 BA FE2 FES . L FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc8 D SG CYS 125 L CYS 125 1_555 BA FE1 FES . L FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc9 I NE2 HIS 86 A HIS 86 1_555 EA FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? 
metalc ? metalc10 I NE2 HIS 100 A HIS 100 1_555 FA FE HEM . A HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? 
metalc ? metalc11 I NE2 HIS 187 A HIS 187 1_555 EA FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc12 I NE2 HIS 202 A HIS 202 1_555 FA FE HEM . A HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? 
metalc ? metalc13 K N TYR 1 C TYR 1 1_555 NA FE HEC . C HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? 
metalc ? metalc14 K NE2 HIS 25 C HIS 25 1_555 NA FE HEC . C HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
metalc ? metalc15 L SG CYS 107 D CYS 107 1_555 PA FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc16 L ND1 HIS 109 D HIS 109 1_555 PA FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc17 L SG CYS 125 D CYS 125 1_555 PA FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc18 L ND1 HIS 128 D HIS 128 1_555 PA FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
#
_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                     6RQF 
_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
Q 9 HEM I 1 301 6 HEM HEM . 
R 9 HEM I 1 302 7 HEM HEM . 
S 10 HEC I 1 303 8 HEC HEM . 
T 11 CLA I 1 304 1 CLA CLA . 
U 12 BCR I 1 305 2 BCR BCR . 
V 13 PL9 I 1 306 2 PL9 PL9 . 
W 14 6PL I 1 307 3 6PL 6PL . 
X 15 LMG J 1 201 1 LMG LMG . 
Y 16 PGV J 1 202 2 PGV PGV . 
Z 10 HEC K 1 301 2 HEC HEM . 
AA 16 PGV K 1 302 4 PGV PGV . 
BA 17 FES L 1 201 2 FES FES . 
CA 18 SQD L 1 202 1 SQD SQD . 
DA 14 6PL N 1 101 1 6PL 6PL . 
EA 9 HEM A 1 301 3 HEM HEM . 
FA 9 HEM A 1 302 4 HEM HEM . 
GA 10 HEC A 1 303 5 HEC HEM . 
HA 11 CLA A 1 304 2 CLA CLA . 
IA 13 PL9 A 1 305 1 PL9 PL9 . 
JA 13 PL9 A 1 306 3 PL9 PL9 . 
KA 18 SQD A 1 307 3 SQD SQD . 
LA 16 PGV A 1 308 3 PGV PGV . 
MA 16 PGV B 1 201 1 PGV PGV . 
NA 10 HEC C 1 301 1 HEC HEM . 
OA 18 SQD C 1 302 2 SQD SQD . 
PA 17 FES D 1 201 1 FES FES . 
QA 14 6PL E 1 101 2 6PL 6PL . 
RA 15 LMG F 1 101 2 LMG LMG . 
SA 12 BCR H 1 101 1 BCR BCR . 
#
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 . . . Y 16 131.966 151.988 202.611 1 58.53 ? P PGV 202 J 1 
HETATM 2 C C01 PGV . . . Y 16 131.255 155.758 200.871 1 58.53 ? C01 PGV 202 J 1 
HETATM 3 C C02 PGV . . . Y 16 131.505 154.611 199.906 1 58.53 ? C02 PGV 202 J 1 
HETATM 4 C C03 PGV . . . Y 16 132.445 153.607 200.565 1 58.53 ? C03 PGV 202 J 1 
HETATM 5 C C04 PGV . . . Y 16 130.415 150.933 204.472 1 58.53 ? C04 PGV 202 J 1 
HETATM 6 C C05 PGV . . . Y 16 129.838 151.312 205.83 1 58.53 ? C05 PGV 202 J 1 
HETATM 7 C C06 PGV . . . Y 16 130.889 152.076 206.621 1 58.53 ? C06 PGV 202 J 1 
HETATM 8 O O01 PGV . . . Y 16 132.085 155.172 198.73 1 58.53 ? O01 PGV 202 J 1 
HETATM 9 O O02 PGV . . . Y 16 131.222 153.424 197.487 1 58.53 ? O02 PGV 202 J 1 
HETATM 10 O O03 PGV . . . Y 16 131.84 156.929 200.315 1 58.53 ? O03 PGV 202 J 1 
HETATM 11 O O04 PGV . . . Y 16 131.22 159.142 200.283 1 58.53 ? O04 PGV 202 J 1 
HETATM 12 O O05 PGV . . . Y 16 129.463 150.136 206.554 1 58.53 ? O05 PGV 202 J 1 
HETATM 13 O O06 PGV . . . Y 16 130.543 152.034 208.006 1 58.53 ? O06 PGV 202 J 1 
HETATM 14 O O11 PGV . . . Y 16 132.06 153.441 201.927 1 58.53 ? O11 PGV 202 J 1 
HETATM 15 O O12 PGV . . . Y 16 130.998 152.093 203.889 1 58.53 ? O12 PGV 202 J 1 
HETATM 16 O O13 PGV . . . Y 16 133.336 151.546 203.049 1 58.53 ? O13 PGV 202 J 1 
HETATM 17 O O14 PGV . . . Y 16 131.378 150.994 201.648 1 58.53 ? O14 PGV 202 J 1 
HETATM 18 C C1 PGV . . . Y 16 131.635 154.57 197.482 1 58.53 ? C1 PGV 202 J 1 
HETATM 19 C C2 PGV . . . Y 16 131.678 155.372 196.198 1 58.53 ? C2 PGV 202 J 1 
HETATM 20 C C3 PGV . . . Y 16 132.912 155.024 195.372 1 58.53 ? C3 PGV 202 J 1 
HETATM 21 C C4 PGV . . . Y 16 133.003 155.876 194.11 1 58.53 ? C4 PGV 202 J 1 
HETATM 22 C C5 PGV . . . Y 16 131.931 155.477 193.105 1 58.53 ? C5 PGV 202 J 1 
HETATM 23 C C6 PGV . . . Y 16 131.927 156.369 191.868 1 58.53 ? C6 PGV 202 J 1 
HETATM 24 C C7 PGV . . . Y 16 133.097 156.055 190.95 1 58.53 ? C7 PGV 202 J 1 
HETATM 25 C C8 PGV . . . Y 16 132.841 156.555 189.533 1 58.53 ? C8 PGV 202 J 1 
HETATM 26 C C9 PGV . . . Y 16 132.06 155.537 188.71 1 58.53 ? C9 PGV 202 J 1 
HETATM 27 C C10 PGV . . . Y 16 131.921 155.991 187.261 1 58.53 ? C10 PGV 202 J 1 
HETATM 28 C C11 PGV . . . Y 16 131.208 157.321 187.231 1 58.53 ? C11 PGV 202 J 1 
HETATM 29 C C12 PGV . . . Y 16 130.423 157.704 186.225 1 58.53 ? C12 PGV 202 J 1 
HETATM 30 C C13 PGV . . . Y 16 130.164 156.85 185.011 1 58.53 ? C13 PGV 202 J 1 
HETATM 31 C C14 PGV . . . Y 16 128.837 157.278 184.391 1 58.53 ? C14 PGV 202 J 1 
HETATM 32 C C15 PGV . . . Y 16 128.613 156.601 183.044 1 58.53 ? C15 PGV 202 J 1 
HETATM 33 C C16 PGV . . . Y 16 127.323 157.061 182.372 1 58.53 ? C16 PGV 202 J 1 
HETATM 34 C C17 PGV . . . Y 16 126.085 156.556 183.1 1 58.53 ? C17 PGV 202 J 1 
HETATM 35 C C18 PGV . . . Y 16 124.848 156.73 182.246 1 58.53 ? C18 PGV 202 J 1 
HETATM 36 C C19 PGV . . . Y 16 130.996 158.021 199.866 1 58.53 ? C19 PGV 202 J 1 
HETATM 37 C C20 PGV . . . Y 16 129.858 157.771 198.907 1 58.53 ? C20 PGV 202 J 1 
HETATM 38 C C21 PGV . . . Y 16 129.476 159.051 198.176 1 58.53 ? C21 PGV 202 J 1 
HETATM 39 C C22 PGV . . . Y 16 130.453 159.332 197.043 1 58.53 ? C22 PGV 202 J 1 
HETATM 40 C C23 PGV . . . Y 16 129.836 160.247 195.996 1 58.53 ? C23 PGV 202 J 1 
HETATM 41 C C24 PGV . . . Y 16 130.802 160.482 194.843 1 58.53 ? C24 PGV 202 J 1 
HETATM 42 C C25 PGV . . . Y 16 130.147 161.329 193.76 1 58.53 ? C25 PGV 202 J 1 
HETATM 43 C C26 PGV . . . Y 16 131.188 161.882 192.797 1 58.53 ? C26 PGV 202 J 1 
HETATM 44 C C27 PGV . . . Y 16 131.177 161.138 191.469 1 58.53 ? C27 PGV 202 J 1 
HETATM 45 C C28 PGV . . . Y 16 132.093 161.84 190.477 1 58.53 ? C28 PGV 202 J 1 
HETATM 46 C C29 PGV . . . Y 16 131.92 161.299 189.065 1 58.53 ? C29 PGV 202 J 1 
HETATM 47 C C30 PGV . . . Y 16 130.664 161.849 188.399 1 58.53 ? C30 PGV 202 J 1 
HETATM 48 C C31 PGV . . . Y 16 129.684 160.726 188.079 1 58.53 ? C31 PGV 202 J 1 
HETATM 49 C C32 PGV . . . Y 16 128.858 161.015 186.83 1 58.53 ? C32 PGV 202 J 1 
HETATM 50 C C33 PGV . . . Y 16 127.8 162.078 187.09 1 58.53 ? C33 PGV 202 J 1 
HETATM 51 C C34 PGV . . . Y 16 126.834 161.638 188.168 1 58.53 ? C34 PGV 202 J 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    205 
_model_server_stats.query_time_ms           416 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           51 
#