data_8DDV
#
_model_server_result.job_id            cJnZSMJJDhZgM2JCFVgmkQ 
_model_server_result.datetime_utc      '2024-12-26 15:00:57' 
_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          8ddv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1401}' 
#
_entry.id    8DDV 
#
_exptl.entry_id    8DDV 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              704.998 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE 
_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            8DDV 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DDV 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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
? 3 I N N 
? 3 N N N 
? 3 Q N N 
? 3 U N N 
#
_chem_comp.formula           'C39 H77 O8 P' 
_chem_comp.formula_weight    704.998 
_chem_comp.id                3PH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE 
_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
O13 P 3PH sing 1 n n 
O13 H13 3PH sing 2 n n 
P O14 3PH sing 3 n n 
P O12 3PH doub 4 n n 
P O11 3PH sing 5 n n 
O11 C1 3PH sing 6 n n 
C1 C2 3PH sing 7 n n 
C1 H11 3PH sing 8 n n 
C1 H12 3PH sing 9 n n 
C2 O21 3PH sing 10 n n 
C2 C3 3PH sing 11 n n 
C2 H2 3PH sing 12 n n 
O21 C21 3PH sing 13 n n 
C21 O22 3PH doub 14 n n 
C21 C22 3PH sing 15 n n 
C22 C23 3PH sing 16 n n 
C22 H221 3PH sing 17 n n 
C22 H222 3PH sing 18 n n 
C23 C24 3PH sing 19 n n 
C23 H231 3PH sing 20 n n 
C23 H232 3PH sing 21 n n 
C24 C25 3PH sing 22 n n 
C24 H241 3PH sing 23 n n 
C24 H242 3PH sing 24 n n 
C25 C26 3PH sing 25 n n 
C25 H251 3PH sing 26 n n 
C25 H252 3PH sing 27 n n 
C26 C27 3PH sing 28 n n 
C26 H261 3PH sing 29 n n 
C26 H262 3PH sing 30 n n 
C27 C28 3PH sing 31 n n 
C27 H271 3PH sing 32 n n 
C27 H272 3PH sing 33 n n 
C28 C29 3PH sing 34 n n 
C28 H281 3PH sing 35 n n 
C28 H282 3PH sing 36 n n 
C29 C2A 3PH sing 37 n n 
C29 H291 3PH sing 38 n n 
C29 H292 3PH sing 39 n n 
C2A C2B 3PH sing 40 n n 
C2A H2A1 3PH sing 41 n n 
C2A H2A2 3PH sing 42 n n 
C2B C2C 3PH sing 43 n n 
C2B H2B1 3PH sing 44 n n 
C2B H2B2 3PH sing 45 n n 
C2C C2D 3PH sing 46 n n 
C2C H2C1 3PH sing 47 n n 
C2C H2C2 3PH sing 48 n n 
C2D C2E 3PH sing 49 n n 
C2D H2D1 3PH sing 50 n n 
C2D H2D2 3PH sing 51 n n 
C2E C2F 3PH sing 52 n n 
C2E H2E1 3PH sing 53 n n 
C2E H2E2 3PH sing 54 n n 
C2F C2G 3PH sing 55 n n 
C2F H2F1 3PH sing 56 n n 
C2F H2F2 3PH sing 57 n n 
C2G C2H 3PH sing 58 n n 
C2G H2G1 3PH sing 59 n n 
C2G H2G2 3PH sing 60 n n 
C2H C2I 3PH sing 61 n n 
C2H H2H1 3PH sing 62 n n 
C2H H2H2 3PH sing 63 n n 
C2I H2I1 3PH sing 64 n n 
C2I H2I2 3PH sing 65 n n 
C2I H2I3 3PH sing 66 n n 
C3 O31 3PH sing 67 n n 
C3 H31 3PH sing 68 n n 
C3 H32 3PH sing 69 n n 
O31 C31 3PH sing 70 n n 
C31 O32 3PH doub 71 n n 
C31 C32 3PH sing 72 n n 
C32 C33 3PH sing 73 n n 
C32 H321 3PH sing 74 n n 
C32 H322 3PH sing 75 n n 
C33 C34 3PH sing 76 n n 
C33 H331 3PH sing 77 n n 
C33 H332 3PH sing 78 n n 
C34 C35 3PH sing 79 n n 
C34 H341 3PH sing 80 n n 
C34 H342 3PH sing 81 n n 
C35 C36 3PH sing 82 n n 
C35 H351 3PH sing 83 n n 
C35 H352 3PH sing 84 n n 
C36 C37 3PH sing 85 n n 
C36 H361 3PH sing 86 n n 
C36 H362 3PH sing 87 n n 
C37 C38 3PH sing 88 n n 
C37 H371 3PH sing 89 n n 
C37 H372 3PH sing 90 n n 
C38 C39 3PH sing 91 n n 
C38 H381 3PH sing 92 n n 
C38 H382 3PH sing 93 n n 
C39 C3A 3PH sing 94 n n 
C39 H391 3PH sing 95 n n 
C39 H392 3PH sing 96 n n 
C3A C3B 3PH sing 97 n n 
C3A H3A1 3PH sing 98 n n 
C3A H3A2 3PH sing 99 n n 
C3B C3C 3PH sing 100 n n 
C3B H3B1 3PH sing 101 n n 
C3B H3B2 3PH sing 102 n n 
C3C C3D 3PH sing 103 n n 
C3C H3C1 3PH sing 104 n n 
C3C H3C2 3PH sing 105 n n 
C3D C3E 3PH sing 106 n n 
C3D H3D1 3PH sing 107 n n 
C3D H3D2 3PH sing 108 n n 
C3E C3F 3PH sing 109 n n 
C3E H3E1 3PH sing 110 n n 
C3E H3E2 3PH sing 111 n n 
C3F C3G 3PH sing 112 n n 
C3F H3F1 3PH sing 113 n n 
C3F H3F2 3PH sing 114 n n 
C3G C3H 3PH sing 115 n n 
C3G H3G1 3PH sing 116 n n 
C3G H3G2 3PH sing 117 n n 
C3H C3I 3PH sing 118 n n 
C3H H3H1 3PH sing 119 n n 
C3H H3H2 3PH sing 120 n n 
C3I H3I1 3PH sing 121 n n 
C3I H3I2 3PH sing 122 n n 
C3I H3I3 3PH sing 123 n n 
O14 H77 3PH sing 124 n n 
#
_atom_sites.entry_id                     8DDV 
_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
I 3 3PH A 1 1401 1401 3PH 3PH . 
J 4 9Z9 A 1 1402 1402 9Z9 9Z9 . 
K 5 PIO A 1 1403 1403 PIO PIO . 
L 4 9Z9 A 1 1404 1402 9Z9 9Z9 . 
M 6 NA A 1 1405 2 NA NA . 
N 3 3PH B 1 1401 1401 3PH 3PH . 
O 5 PIO B 1 1402 1403 PIO PIO . 
P 4 9Z9 C 1 1401 1402 9Z9 9Z9 . 
Q 3 3PH C 1 1402 1401 3PH 3PH . 
R 4 9Z9 C 1 1403 1402 9Z9 9Z9 . 
S 5 PIO C 1 1404 1403 PIO PIO . 
T 6 NA C 1 1405 1 NA NA . 
U 3 3PH D 1 1401 1401 3PH 3PH . 
V 5 PIO D 1 1402 1403 PIO PIO . 
#
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 O O13 3PH . . . I 3 236.546 201.949 221.335 1 17.3 ? O13 3PH 1401 A 1 
HETATM 2 P P 3PH . . . I 3 236.092 203.253 221.959 1 17.3 ? P 3PH 1401 A 1 
HETATM 3 O O14 3PH . . . I 3 236.927 203.543 223.185 1 17.3 ? O14 3PH 1401 A 1 
HETATM 4 O O12 3PH . . . I 3 236.258 204.38 220.963 1 17.3 ? O12 3PH 1401 A 1 
HETATM 5 O O11 3PH . . . I 3 234.496 203.131 222.391 1 17.3 ? O11 3PH 1401 A 1 
HETATM 6 C C1 3PH . . . I 3 233.912 204.195 223.118 1 17.3 ? C1 3PH 1401 A 1 
HETATM 7 C C2 3PH . . . I 3 233.226 204.241 224.491 1 17.3 ? C2 3PH 1401 A 1 
HETATM 8 O O21 3PH . . . I 3 231.84 204.342 224.308 1 17.3 ? O21 3PH 1401 A 1 
HETATM 9 C C21 3PH . . . I 3 231.065 203.55 225.197 1 17.3 ? C21 3PH 1401 A 1 
HETATM 10 O O22 3PH . . . I 3 230.758 202.444 224.894 1 17.3 ? O22 3PH 1401 A 1 
HETATM 11 C C22 3PH . . . I 3 230.617 204.134 226.561 1 17.3 ? C22 3PH 1401 A 1 
HETATM 12 C C23 3PH . . . I 3 229.144 203.744 226.849 1 17.3 ? C23 3PH 1401 A 1 
HETATM 13 C C24 3PH . . . I 3 229.076 203.032 228.228 1 17.3 ? C24 3PH 1401 A 1 
HETATM 14 C C25 3PH . . . I 3 229.424 204.049 229.353 1 17.3 ? C25 3PH 1401 A 1 
HETATM 15 C C26 3PH . . . I 3 228.287 204.039 230.413 1 17.3 ? C26 3PH 1401 A 1 
HETATM 16 C C27 3PH . . . I 3 228.905 204.143 231.836 1 17.3 ? C27 3PH 1401 A 1 
HETATM 17 C C28 3PH . . . I 3 228.46 205.473 232.505 1 17.3 ? C28 3PH 1401 A 1 
HETATM 18 C C29 3PH . . . I 3 227.735 205.148 233.838 1 17.3 ? C29 3PH 1401 A 1 
HETATM 19 C C2A 3PH . . . I 3 228.638 205.52 235.045 1 17.3 ? C2A 3PH 1401 A 1 
HETATM 20 C C2B 3PH . . . I 3 227.873 205.205 236.36 1 17.3 ? C2B 3PH 1401 A 1 
HETATM 21 C C2C 3PH . . . I 3 228.707 205.663 237.588 1 17.3 ? C2C 3PH 1401 A 1 
HETATM 22 C C2D 3PH . . . I 3 227.804 205.652 238.853 1 17.3 ? C2D 3PH 1401 A 1 
HETATM 23 C C2E 3PH . . . I 3 227.156 204.248 239.013 1 17.3 ? C2E 3PH 1401 A 1 
HETATM 24 C C2F 3PH . . . I 3 226.809 203.995 240.506 1 17.3 ? C2F 3PH 1401 A 1 
HETATM 25 C C3 3PH . . . I 3 233.741 205.456 225.272 1 17.3 ? C3 3PH 1401 A 1 
HETATM 26 O O31 3PH . . . I 3 234.735 205.048 226.191 1 17.3 ? O31 3PH 1401 A 1 
HETATM 27 C C31 3PH . . . I 3 234.263 204.872 227.514 1 17.3 ? C31 3PH 1401 A 1 
HETATM 28 O O32 3PH . . . I 3 233.616 203.915 227.792 1 17.3 ? O32 3PH 1401 A 1 
HETATM 29 C C32 3PH . . . I 3 234.593 205.918 228.603 1 17.3 ? C32 3PH 1401 A 1 
HETATM 30 C C33 3PH . . . I 3 234.823 205.198 229.957 1 17.3 ? C33 3PH 1401 A 1 
HETATM 31 C C34 3PH . . . I 3 233.515 205.23 230.795 1 17.3 ? C34 3PH 1401 A 1 
HETATM 32 C C35 3PH . . . I 3 233.809 205.845 232.191 1 17.3 ? C35 3PH 1401 A 1 
HETATM 33 C C36 3PH . . . I 3 233.428 204.82 233.292 1 17.3 ? C36 3PH 1401 A 1 
HETATM 34 C C37 3PH . . . I 3 233.942 205.317 234.672 1 17.3 ? C37 3PH 1401 A 1 
HETATM 35 C C38 3PH . . . I 3 232.752 205.396 235.667 1 17.3 ? C38 3PH 1401 A 1 
HETATM 36 C C39 3PH . . . I 3 233.253 205.084 237.104 1 17.3 ? C39 3PH 1401 A 1 
HETATM 37 C C3A 3PH . . . I 3 233.759 206.392 237.774 1 17.3 ? C3A 3PH 1401 A 1 
HETATM 38 C C3B 3PH . . . I 3 234.166 206.094 239.243 1 17.3 ? C3B 3PH 1401 A 1 
HETATM 39 C C3C 3PH . . . I 3 235.58 205.448 239.267 1 17.3 ? C3C 3PH 1401 A 1 
HETATM 40 C C3D 3PH . . . I 3 236.666 206.56 239.184 1 17.3 ? C3D 3PH 1401 A 1 
HETATM 41 C C3E 3PH . . . I 3 238.081 205.91 239.141 1 17.3 ? C3E 3PH 1401 A 1 
HETATM 42 C C3F 3PH . . . I 3 238.315 205.235 237.759 1 17.3 ? C3F 3PH 1401 A 1 
HETATM 43 C C3G 3PH . . . I 3 238.666 206.324 236.707 1 17.3 ? C3G 3PH 1401 A 1 
HETATM 44 C C3H 3PH . . . I 3 237.569 206.354 235.613 1 17.3 ? C3H 3PH 1401 A 1 
HETATM 45 C C3I 3PH . . . I 3 237.632 207.701 234.858 1 17.3 ? C3I 3PH 1401 A 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           36 
_model_server_stats.create_model_time_ms    104 
_model_server_stats.query_time_ms           348 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           45 
#