data_8YHQ
#
_model_server_result.job_id            0cp3wb3OCWm_TNzWHaGjdQ 
_model_server_result.datetime_utc      '2024-12-26 13:25:38' 
_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":"U","auth_seq_id":401}' 
#
_entry.id    8YHQ 
#
_exptl.entry_id    8YHQ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              592.785 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate' 
_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
? 11 U N N 
? 11 LA 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           'C31 H61 O8 P' 
_chem_comp.formula_weight    592.785 
_chem_comp.id                6PH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate' 
_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
P O11 6PH sing 1 n n 
P O13 6PH sing 2 n n 
O11 C1 6PH sing 3 n n 
O12 P 6PH doub 4 n n 
O13 HO13 6PH sing 5 n n 
O14 P 6PH sing 6 n n 
O14 HO14 6PH sing 7 n n 
C1 H1 6PH sing 8 n n 
C1 H1A 6PH sing 9 n n 
C2 C1 6PH sing 10 n n 
C2 H2 6PH sing 11 n n 
C3 C2 6PH sing 12 n n 
C3 H3 6PH sing 13 n n 
C3 H3A 6PH sing 14 n n 
O31 C3 6PH sing 15 n n 
O32 C31 6PH doub 16 n n 
C31 O31 6PH sing 17 n n 
C32 C31 6PH sing 18 n n 
C32 H32 6PH sing 19 n n 
C32 H32A 6PH sing 20 n n 
C33 C32 6PH sing 21 n n 
C33 C34 6PH sing 22 n n 
C33 H33 6PH sing 23 n n 
C33 H33A 6PH sing 24 n n 
C34 C35 6PH sing 25 n n 
C34 H34 6PH sing 26 n n 
C34 H34A 6PH sing 27 n n 
C35 H35 6PH sing 28 n n 
C35 H35A 6PH sing 29 n n 
C36 C35 6PH sing 30 n n 
C36 C37 6PH sing 31 n n 
C36 H36 6PH sing 32 n n 
C36 H36A 6PH sing 33 n n 
C37 H37 6PH sing 34 n n 
C37 H37A 6PH sing 35 n n 
C38 C37 6PH sing 36 n n 
C38 C39 6PH sing 37 n n 
C38 H38 6PH sing 38 n n 
C38 H38A 6PH sing 39 n n 
C39 C3A 6PH sing 40 n n 
C39 H39 6PH sing 41 n n 
C39 H39A 6PH sing 42 n n 
C3A H3AA 6PH sing 43 n n 
C3A H3AB 6PH sing 44 n n 
C3B C3A 6PH sing 45 n n 
C3B C3C 6PH sing 46 n n 
C3B H3B 6PH sing 47 n n 
C3B H3BA 6PH sing 48 n n 
C3C C3D 6PH sing 49 n n 
C3C H3C 6PH sing 50 n n 
C3C H3CA 6PH sing 51 n n 
C3D H3D 6PH sing 52 n n 
C3D H3DA 6PH sing 53 n n 
C3D H3DB 6PH sing 54 n n 
O21 C2 6PH sing 55 n n 
O21 C21 6PH sing 56 n n 
C21 O22 6PH doub 57 n n 
C22 C21 6PH sing 58 n n 
C22 C23 6PH sing 59 n n 
C22 H22 6PH sing 60 n n 
C22 H22A 6PH sing 61 n n 
C23 H23 6PH sing 62 n n 
C23 H23A 6PH sing 63 n n 
C24 C23 6PH sing 64 n n 
C24 C25 6PH sing 65 n n 
C24 H24 6PH sing 66 n n 
C24 H24A 6PH sing 67 n n 
C25 H25 6PH sing 68 n n 
C25 H25A 6PH sing 69 n n 
C26 C25 6PH sing 70 n n 
C26 H26 6PH sing 71 n n 
C26 H26A 6PH sing 72 n n 
C27 C26 6PH sing 73 n n 
C27 H27 6PH sing 74 n n 
C27 H27A 6PH sing 75 n n 
C28 C27 6PH sing 76 n n 
C28 H28 6PH sing 77 n n 
C28 H28A 6PH sing 78 n n 
C29 C28 6PH sing 79 n n 
C29 H29 6PH sing 80 n n 
C29 H29A 6PH sing 81 n n 
C2A C29 6PH sing 82 n n 
C2A C2B 6PH sing 83 n n 
C2A H2A 6PH sing 84 n n 
C2A H2AA 6PH sing 85 n n 
C2B C2C 6PH sing 86 n n 
C2B H2B 6PH sing 87 n n 
C2C C2D 6PH sing 88 n n 
C2C H2C 6PH sing 89 n n 
C2D C2E 6PH sing 90 n n 
C2D H2D 6PH sing 91 n n 
C2D H2DA 6PH sing 92 n n 
C2E C2F 6PH sing 93 n n 
C2E H2E 6PH sing 94 n n 
C2F H2F 6PH sing 95 n n 
C2F H2FA 6PH sing 96 n n 
C2B H58 6PH sing 97 n n 
C2C H59 6PH sing 98 n n 
C2E H60 6PH sing 99 n n 
C2F H61 6PH sing 100 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 6PH . . . U 11 132.694 108.239 135.679 1 31.15 ? P 6PH 401 C 1 
HETATM 2 O O11 6PH . . . U 11 133.622 107.332 134.668 1 31.15 ? O11 6PH 401 C 1 
HETATM 3 O O12 6PH . . . U 11 133.524 108.708 136.848 1 31.15 ? O12 6PH 401 C 1 
HETATM 4 O O13 6PH . . . U 11 132.19 109.427 134.907 1 31.15 ? O13 6PH 401 C 1 
HETATM 5 O O14 6PH . . . U 11 131.521 107.429 136.178 1 31.15 ? O14 6PH 401 C 1 
HETATM 6 C C1 6PH . . . U 11 132.981 106.56 133.694 1 31.15 ? C1 6PH 401 C 1 
HETATM 7 C C2 6PH . . . U 11 132.903 107.309 132.363 1 31.15 ? C2 6PH 401 C 1 
HETATM 8 C C3 6PH . . . U 11 132.383 106.334 131.313 1 31.15 ? C3 6PH 401 C 1 
HETATM 9 O O31 6PH . . . U 11 133.369 106.112 130.352 1 31.15 ? O31 6PH 401 C 1 
HETATM 10 O O32 6PH . . . U 11 134.288 104.077 130.197 1 31.15 ? O32 6PH 401 C 1 
HETATM 11 C C31 6PH . . . U 11 133.391 104.792 129.902 1 31.15 ? C31 6PH 401 C 1 
HETATM 12 C C32 6PH . . . U 11 132.24 104.27 129.047 1 31.15 ? C32 6PH 401 C 1 
HETATM 13 C C33 6PH . . . U 11 132.291 104.922 127.669 1 31.15 ? C33 6PH 401 C 1 
HETATM 14 C C34 6PH . . . U 11 131.471 106.218 127.604 1 31.15 ? C34 6PH 401 C 1 
HETATM 15 C C35 6PH . . . U 11 130.267 106.168 126.648 1 31.15 ? C35 6PH 401 C 1 
HETATM 16 C C36 6PH . . . U 11 130.274 107.374 125.709 1 31.15 ? C36 6PH 401 C 1 
HETATM 17 C C37 6PH . . . U 11 128.857 107.627 125.202 1 31.15 ? C37 6PH 401 C 1 
HETATM 18 C C38 6PH . . . U 11 128.726 108.692 124.098 1 31.15 ? C38 6PH 401 C 1 
HETATM 19 C C39 6PH . . . U 11 129.946 109.6 123.896 1 31.15 ? C39 6PH 401 C 1 
HETATM 20 C C3A 6PH . . . U 11 129.668 110.841 123.032 1 31.15 ? C3A 6PH 401 C 1 
HETATM 21 C C3B 6PH . . . U 11 128.614 110.626 121.947 1 31.15 ? C3B 6PH 401 C 1 
HETATM 22 C C3C 6PH . . . U 11 128.692 111.704 120.871 1 31.15 ? C3C 6PH 401 C 1 
HETATM 23 C C3D 6PH . . . U 11 127.991 112.975 121.334 1 31.15 ? C3D 6PH 401 C 1 
HETATM 24 O O21 6PH . . . U 11 132.03 108.404 132.446 1 31.15 ? O21 6PH 401 C 1 
HETATM 25 O O22 6PH . . . U 11 133.08 110.166 131.553 1 31.15 ? O22 6PH 401 C 1 
HETATM 26 C C21 6PH . . . U 11 132.211 109.372 131.448 1 31.15 ? C21 6PH 401 C 1 
HETATM 27 C C22 6PH . . . U 11 131.305 109.387 130.213 1 31.15 ? C22 6PH 401 C 1 
HETATM 28 C C23 6PH . . . U 11 130.755 110.787 129.922 1 31.15 ? C23 6PH 401 C 1 
HETATM 29 C C24 6PH . . . U 11 130.671 111.104 128.42 1 31.15 ? C24 6PH 401 C 1 
HETATM 30 C C25 6PH . . . U 11 129.265 111.555 128.02 1 31.15 ? C25 6PH 401 C 1 
HETATM 31 C C26 6PH . . . U 11 129.314 112.237 126.648 1 31.15 ? C26 6PH 401 C 1 
HETATM 32 C C27 6PH . . . U 11 129.401 113.76 126.739 1 31.15 ? C27 6PH 401 C 1 
HETATM 33 C C28 6PH . . . U 11 128.725 114.418 125.528 1 31.15 ? C28 6PH 401 C 1 
HETATM 34 C C29 6PH . . . U 11 127.199 114.516 125.638 1 31.15 ? C29 6PH 401 C 1 
HETATM 35 C C2A 6PH . . . U 11 126.778 115.459 126.76 1 31.15 ? C2A 6PH 401 C 1 
HETATM 36 C C2B 6PH . . . U 11 125.274 115.718 126.729 1 31.15 ? C2B 6PH 401 C 1 
HETATM 37 C C2C 6PH . . . U 11 124.99 117.199 126.962 1 31.15 ? C2C 6PH 401 C 1 
HETATM 38 C C2D 6PH . . . U 11 125.245 117.601 128.415 1 31.15 ? C2D 6PH 401 C 1 
HETATM 39 C C2E 6PH . . . U 11 125.735 119.043 128.462 1 31.15 ? C2E 6PH 401 C 1 
HETATM 40 C C2F 6PH . . . U 11 127.248 119.091 128.297 1 31.15 ? C2F 6PH 401 C 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    59 
_model_server_stats.query_time_ms           399 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           40 
#