data_8YHQ
#
_model_server_result.job_id            8eAGt74MOIRBHcE_nAs_oQ 
_model_server_result.datetime_utc      '2024-12-26 13:33:15' 
_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          8yhq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DA","auth_seq_id":402}' 
#
_entry.id    8YHQ 
#
_exptl.entry_id    8YHQ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              564.732 
_entity.id                          18 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate' 
_entity.pdbx_number_of_molecules    2 
_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            8YHQ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YHQ 
_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    eicosameric 
_pdbx_struct_assembly.oligomeric_count      20 
_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 
_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
? 18 DA N N 
? 18 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 E SG CYS 129 E CYS 159 1_555 E SG CYS 134 E CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? 
disulf ? disulf2 E SG CYS 148 E CYS 178 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? 
disulf ? disulf3 F SG CYS 29 F CYS 101 1_555 F SG CYS 51 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? 
disulf ? disulf4 N SG CYS 134 N CYS 164 1_555 N SG CYS 150 N CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? 
disulf ? disulf5 P SG CYS 29 O CYS 101 1_555 P SG CYS 51 O CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? 
metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc6 G NE2 HIS 82 L HIS 82 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc7 G NE2 HIS 96 L HIS 96 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? 
metalc ? metalc8 G NE2 HIS 183 L HIS 183 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc9 G NE2 HIS 197 L HIS 197 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? 
metalc ? metalc10 M NE2 HIS 44 M HIS 105 1_555 KA FE HEM . M HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
#
_chem_comp.formula           'C29 H57 O8 P' 
_chem_comp.formula_weight    564.732 
_chem_comp.id                7PH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'PHOSPHATIDIC ACID' 
#
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
O11 P 7PH sing 101 n n 
O14 P 7PH doub 102 n n 
P O13 7PH sing 103 n n 
P O12 7PH sing 104 n n 
O12 HO12 7PH sing 105 n n 
O13 HO13 7PH sing 106 n n 
C1 O11 7PH sing 107 n n 
C2 C1 7PH sing 108 n n 
C1 H1 7PH sing 109 n n 
C1 H1A 7PH sing 110 n n 
C3 C2 7PH sing 111 n n 
C2 O21 7PH sing 112 n n 
C2 H2 7PH sing 113 n n 
O31 C3 7PH sing 114 n n 
C3 H3 7PH sing 115 n n 
C3 H3A 7PH sing 116 n n 
C31 O31 7PH sing 117 n n 
C31 O32 7PH doub 118 n n 
C32 C31 7PH sing 119 n n 
C33 C32 7PH sing 120 n n 
C32 H32 7PH sing 121 n n 
C32 H32A 7PH sing 122 n n 
C33 C34 7PH sing 123 n n 
C33 H33 7PH sing 124 n n 
C33 H33A 7PH sing 125 n n 
C34 C35 7PH sing 126 n n 
C34 H34 7PH sing 127 n n 
C34 H34A 7PH sing 128 n n 
C35 C36 7PH sing 129 n n 
C35 H35 7PH sing 130 n n 
C35 H35A 7PH sing 131 n n 
C36 C37 7PH sing 132 n n 
C36 H36 7PH sing 133 n n 
C36 H36A 7PH sing 134 n n 
C37 C38 7PH sing 135 n n 
C37 H37 7PH sing 136 n n 
C37 H37A 7PH sing 137 n n 
C38 C39 7PH sing 138 n n 
C38 H38 7PH sing 139 n n 
C38 H38A 7PH sing 140 n n 
C39 C3A 7PH sing 141 n n 
C39 H39 7PH sing 142 n n 
C39 H39A 7PH sing 143 n n 
C3A C3B 7PH sing 144 n n 
C3A H3AA 7PH sing 145 n n 
C3A H3AB 7PH sing 146 n n 
C3B C3C 7PH sing 147 n n 
C3B H3B 7PH sing 148 n n 
C3B H3BA 7PH sing 149 n n 
C3C H3C 7PH sing 150 n n 
C3C H3CA 7PH sing 151 n n 
C3C H3CB 7PH sing 152 n n 
C21 O21 7PH sing 153 n n 
O22 C21 7PH doub 154 n n 
C21 C22 7PH sing 155 n n 
C23 C22 7PH sing 156 n n 
C22 H22 7PH sing 157 n n 
C22 H22A 7PH sing 158 n n 
C24 C23 7PH sing 159 n n 
C23 H23 7PH sing 160 n n 
C23 H23A 7PH sing 161 n n 
C25 C24 7PH sing 162 n n 
C24 H24 7PH sing 163 n n 
C24 H24A 7PH sing 164 n n 
C26 C25 7PH sing 165 n n 
C25 H25 7PH sing 166 n n 
C25 H25A 7PH sing 167 n n 
C27 C26 7PH sing 168 n n 
C26 H26 7PH sing 169 n n 
C26 H26A 7PH sing 170 n n 
C27 C28 7PH sing 171 n n 
C27 H27 7PH sing 172 n n 
C27 H27A 7PH sing 173 n n 
C28 C29 7PH sing 174 n n 
C28 H28 7PH sing 175 n n 
C28 H28A 7PH sing 176 n n 
C29 C2A 7PH sing 177 n n 
C29 H29 7PH sing 178 n n 
C29 H29A 7PH sing 179 n n 
C2A C2B 7PH sing 180 n n 
C2A H2A 7PH sing 181 n n 
C2A H2AA 7PH sing 182 n n 
C2B C2C 7PH sing 183 n n 
C2B H2B 7PH sing 184 n n 
C2B H2BA 7PH sing 185 n n 
C2C C2D 7PH sing 186 n n 
C2C H2C 7PH sing 187 n n 
C2C H2CA 7PH sing 188 n n 
C2D C2E 7PH sing 189 n n 
C2D H2D 7PH sing 190 n n 
C2D H2DA 7PH sing 191 n n 
C2E H2E 7PH sing 192 n n 
C2E H2EA 7PH sing 193 n n 
C2E H2EB 7PH sing 194 n n 
#
_atom_sites.entry_id                     8YHQ 
_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
U 11 6PH C 1 401 402 6PH 6PH . 
V 12 9PE C 1 402 403 9PE 9PE . 
W 13 HEM C 1 403 404 HEM HEM . 
X 13 HEM C 1 404 405 HEM HEM . 
Y 14 8PE C 1 405 406 8PE 8PE . 
Z 15 CN5 C 1 406 407 CN5 CN5 . 
AA 16 UQ6 C 1 407 408 UQ6 UQ6 . 
BA 17 A1D6K C 1 408 401 A1D6K A1D . 
CA 13 HEM D 1 401 402 HEM HEM . 
DA 18 7PH D 1 402 401 7PH 7PH . 
EA 16 UQ6 L 1 401 402 UQ6 UQ6 . 
FA 12 9PE L 1 402 403 9PE 9PE . 
GA 13 HEM L 1 403 404 HEM HEM . 
HA 19 CN3 L 1 404 405 CN3 CN3 . 
IA 13 HEM L 1 405 406 HEM HEM . 
JA 17 A1D6K L 1 406 401 A1D6K A1D . 
KA 13 HEM M 1 401 401 HEM HEM . 
LA 11 6PH N 1 401 401 6PH 6PH . 
MA 18 7PH N 1 402 402 7PH 7PH . 
NA 14 8PE Q 1 101 101 8PE 8PE . 
#
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 7PH . . . DA 18 130.871 105.605 106.409 1 24.97 ? P 7PH 402 D 1 
HETATM 2 O O12 7PH . . . DA 18 131.531 106.903 106.167 1 24.97 ? O12 7PH 402 D 1 
HETATM 3 O O13 7PH . . . DA 18 130.19 105.151 105.202 1 24.97 ? O13 7PH 402 D 1 
HETATM 4 O O14 7PH . . . DA 18 131.836 104.595 106.901 1 24.97 ? O14 7PH 402 D 1 
HETATM 5 O O11 7PH . . . DA 18 129.685 105.882 107.445 1 24.97 ? O11 7PH 402 D 1 
HETATM 6 C C1 7PH . . . DA 18 128.585 106.734 107.015 1 24.97 ? C1 7PH 402 D 1 
HETATM 7 C C2 7PH . . . DA 18 128.29 107.858 107.986 1 24.97 ? C2 7PH 402 D 1 
HETATM 8 C C3 7PH . . . DA 18 128.738 107.531 109.392 1 24.97 ? C3 7PH 402 D 1 
HETATM 9 O O31 7PH . . . DA 18 127.841 106.538 109.945 1 24.97 ? O31 7PH 402 D 1 
HETATM 10 O O32 7PH . . . DA 18 128.31 105.838 111.991 1 24.97 ? O32 7PH 402 D 1 
HETATM 11 C C31 7PH . . . DA 18 127.709 106.559 111.263 1 24.97 ? C31 7PH 402 D 1 
HETATM 12 C C32 7PH . . . DA 18 126.785 107.626 111.718 1 24.97 ? C32 7PH 402 D 1 
HETATM 13 C C33 7PH . . . DA 18 127.481 108.672 112.501 1 24.97 ? C33 7PH 402 D 1 
HETATM 14 C C34 7PH . . . DA 18 126.645 109.199 113.639 1 24.97 ? C34 7PH 402 D 1 
HETATM 15 C C35 7PH . . . DA 18 127.447 109.871 114.702 1 24.97 ? C35 7PH 402 D 1 
HETATM 16 C C36 7PH . . . DA 18 127.838 108.962 115.82 1 24.97 ? C36 7PH 402 D 1 
HETATM 17 C C37 7PH . . . DA 18 127.879 109.613 117.173 1 24.97 ? C37 7PH 402 D 1 
HETATM 18 C C38 7PH . . . DA 18 129.187 110.279 117.5 1 24.97 ? C38 7PH 402 D 1 
HETATM 19 C C39 7PH . . . DA 18 129.764 111.085 116.373 1 24.97 ? C39 7PH 402 D 1 
HETATM 20 C C3A 7PH . . . DA 18 130.975 111.897 116.759 1 24.97 ? C3A 7PH 402 D 1 
HETATM 21 C C3B 7PH . . . DA 18 131.038 113.254 116.133 1 24.97 ? C3B 7PH 402 D 1 
HETATM 22 C C3C 7PH . . . DA 18 132.44 113.771 116.046 1 24.97 ? C3C 7PH 402 D 1 
HETATM 23 O O21 7PH . . . DA 18 128.902 109.084 107.49 1 24.97 ? O21 7PH 402 D 1 
HETATM 24 O O22 7PH . . . DA 18 129.557 110.961 108.457 1 24.97 ? O22 7PH 402 D 1 
HETATM 25 C C21 7PH . . . DA 18 128.666 110.249 108.106 1 24.97 ? C21 7PH 402 D 1 
HETATM 26 C C22 7PH . . . DA 18 127.244 110.652 108.312 1 24.97 ? C22 7PH 402 D 1 
HETATM 27 C C23 7PH . . . DA 18 127.103 112.009 108.91 1 24.97 ? C23 7PH 402 D 1 
HETATM 28 C C24 7PH . . . DA 18 125.659 112.388 109.132 1 24.97 ? C24 7PH 402 D 1 
HETATM 29 C C25 7PH . . . DA 18 125.156 112.088 110.5 1 24.97 ? C25 7PH 402 D 1 
HETATM 30 C C26 7PH . . . DA 18 123.659 112.118 110.644 1 24.97 ? C26 7PH 402 D 1 
HETATM 31 C C27 7PH . . . DA 18 123.104 113.34 111.314 1 24.97 ? C27 7PH 402 D 1 
HETATM 32 C C28 7PH . . . DA 18 123.759 113.692 112.619 1 24.97 ? C28 7PH 402 D 1 
HETATM 33 C C29 7PH . . . DA 18 124.544 114.973 112.603 1 24.97 ? C29 7PH 402 D 1 
HETATM 34 C C2A 7PH . . . DA 18 125.872 114.916 113.278 1 24.97 ? C2A 7PH 402 D 1 
HETATM 35 C C2B 7PH . . . DA 18 126.897 115.817 112.654 1 24.97 ? C2B 7PH 402 D 1 
HETATM 36 C C2C 7PH . . . DA 18 128.13 116.024 113.484 1 24.97 ? C2C 7PH 402 D 1 
HETATM 37 C C2D 7PH . . . DA 18 129.221 116.774 112.779 1 24.97 ? C2D 7PH 402 D 1 
HETATM 38 C C2E 7PH . . . DA 18 129.564 118.114 113.373 1 24.97 ? C2E 7PH 402 D 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           38 
#