data_3TH1
#
_model_server_result.job_id            a0HvsyBoawPxdtk5pYXTTw 
_model_server_result.datetime_utc      '2025-02-28 13:49:09' 
_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          3th1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    3TH1 
#
_exptl.entry_id    3TH1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              704.998 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE 
_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         120 
_cell.entry_id            3TH1 
_cell.length_a            97.57 
_cell.length_b            97.57 
_cell.length_c            423.6 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TH1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,I,P 1 1,2 
B,J,K,L,M,N,Q 2 1 
C,O,R 2 3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
3 'crystal symmetry operation' 5_554 y,-x+y,z-1/6 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 -70.6 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 M 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
metalc ? metalc1 A OH TYR 130 A TYR 130 1_555 D FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc2 A OH TYR 164 A TYR 164 1_555 D FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc3 A NE2 HIS 188 A HIS 188 1_555 D FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc4 A NE2 HIS 190 A HIS 190 1_555 D FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc5 B OH TYR 130 B TYR 130 1_555 K FE FE . B FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? 
metalc ? metalc6 B OH TYR 164 B TYR 164 1_555 K FE FE . B FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc7 B NE2 HIS 188 B HIS 188 1_555 K FE FE . B FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc8 C OH TYR 130 C TYR 130 1_555 O FE FE . C FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? 
metalc ? metalc9 C OH TYR 164 C TYR 164 1_555 O FE FE . C FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? 
metalc ? metalc10 C NE2 HIS 188 C HIS 188 1_555 O FE FE . C FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc11 C NE2 HIS 190 C HIS 190 1_555 O FE FE . C FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
#
_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                     3TH1 
_atom_sites.fract_transf_matrix[1][1]    0.010249 
_atom_sites.fract_transf_matrix[1][2]    0.005917 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011835 
_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]    0.002361 
_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
D 2 FE A 1 300 300 FE FE . 
E 3 DTD A 1 301 301 DTD DTD . 
F 4 3PH A 1 302 302 3PH 3PH . 
G 5 MG A 1 303 303 MG MG . 
H 5 MG A 1 304 304 MG MG . 
I 6 ACT A 1 305 305 ACT ACT . 
J 7 GOL B 1 306 306 GOL GOL . 
K 2 FE B 1 300 300 FE FE . 
L 3 DTD B 1 301 301 DTD DTD . 
M 4 3PH B 1 302 302 3PH 3PH . 
N 7 GOL B 1 303 303 GOL GOL . 
O 2 FE C 1 300 300 FE FE . 
P 8 HOH A 1 261 261 HOH HOH . 
P 8 HOH A 2 262 262 HOH HOH . 
P 8 HOH A 3 263 263 HOH HOH . 
P 8 HOH A 4 264 264 HOH HOH . 
P 8 HOH A 5 265 265 HOH HOH . 
P 8 HOH A 6 266 266 HOH HOH . 
P 8 HOH A 7 267 267 HOH HOH . 
P 8 HOH A 8 268 268 HOH HOH . 
Q 8 HOH B 1 261 261 HOH HOH . 
Q 8 HOH B 2 262 262 HOH HOH . 
Q 8 HOH B 3 263 263 HOH HOH . 
R 8 HOH C 1 261 261 HOH HOH . 
R 8 HOH C 2 262 262 HOH HOH . 
R 8 HOH C 3 263 263 HOH HOH . 
R 8 HOH C 4 264 264 HOH HOH . 
R 8 HOH C 5 265 265 HOH HOH . 
R 8 HOH C 6 266 266 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 O O13 3PH . . . F 4 45.234 -10.034 -9.458 0.59 39.9 1 O13 3PH 302 A 1 
HETATM 2 P P 3PH . . . F 4 44.441 -9.715 -10.666 1 84.57 ? P 3PH 302 A 1 
HETATM 3 O O14 3PH . . . F 4 43.081 -10.582 -10.787 1 85 ? O14 3PH 302 A 1 
HETATM 4 O O12 3PH . . . F 4 43.973 -8.168 -10.733 0.6 31.79 ? O12 3PH 302 A 1 
HETATM 5 O O11 3PH . . . F 4 45.244 -9.981 -12.046 0.97 67.42 ? O11 3PH 302 A 1 
HETATM 6 C C1 3PH . . . F 4 45.623 -8.88 -12.876 0.98 64.64 ? C1 3PH 302 A 1 
HETATM 7 C C2 3PH . . . F 4 47.013 -8.388 -12.469 0.66 60.17 ? C2 3PH 302 A 1 
HETATM 8 O O21 3PH . . . F 4 47.997 -8.975 -13.324 0.34 59.82 ? O21 3PH 302 A 1 
HETATM 9 C C21 3PH . . . F 4 47.955 -8.376 -14.544 0.66 59.44 ? C21 3PH 302 A 1 
HETATM 10 O O22 3PH . . . F 4 47.375 -8.846 -15.521 1 60.51 ? O22 3PH 302 A 1 
HETATM 11 C C22 3PH . . . F 4 48.694 -7.04 -14.634 1 57.18 ? C22 3PH 302 A 1 
HETATM 12 C C23 3PH . . . F 4 50.126 -7.212 -14.123 1 54.62 ? C23 3PH 302 A 1 
HETATM 13 C C24 3PH . . . F 4 50.173 -6.914 -12.624 1 51.17 ? C24 3PH 302 A 1 
HETATM 14 C C25 3PH . . . F 4 51.538 -6.324 -12.263 1 48.56 ? C25 3PH 302 A 1 
HETATM 15 C C26 3PH . . . F 4 51.342 -5.014 -11.498 1 47.19 ? C26 3PH 302 A 1 
HETATM 16 C C27 3PH . . . F 4 52.428 -4.879 -10.429 1 46.15 ? C27 3PH 302 A 1 
HETATM 17 C C28 3PH . . . F 4 51.891 -4.058 -9.255 1 44.77 ? C28 3PH 302 A 1 
HETATM 18 C C29 3PH . . . F 4 51.384 -2.708 -9.766 0.89 43.63 ? C29 3PH 302 A 1 
HETATM 19 C C2A 3PH . . . F 4 50.492 -2.062 -8.704 1 43.06 ? C2A 3PH 302 A 1 
HETATM 20 C C2B 3PH . . . F 4 50.829 -0.574 -8.59 1 42.24 ? C2B 3PH 302 A 1 
HETATM 21 C C2C 3PH . . . F 4 50.097 0.026 -7.387 0.68 39.57 ? C2C 3PH 302 A 1 
HETATM 22 C C2D 3PH . . . F 4 50.777 -0.432 -6.095 0.94 37.01 ? C2D 3PH 302 A 1 
HETATM 23 C C2E 3PH . . . F 4 50.276 0.417 -4.926 0.31 35.43 ? C2E 3PH 302 A 1 
HETATM 24 C C2F 3PH . . . F 4 50.163 -0.454 -3.673 1 33.95 ? C2F 3PH 302 A 1 
HETATM 25 C C2G 3PH . . . F 4 50.921 0.208 -2.521 0 33.32 ? C2G 3PH 302 A 1 
HETATM 26 C C2H 3PH . . . F 4 50.845 -0.685 -1.28 0.48 32.72 ? C2H 3PH 302 A 1 
HETATM 27 C C2I 3PH . . . F 4 51.188 0.138 -0.037 0.88 32.69 ? C2I 3PH 302 A 1 
HETATM 28 C C3 3PH . . . F 4 47.291 -8.788 -11.019 0.4 56.13 ? C3 3PH 302 A 1 
HETATM 29 O O31 3PH . . . F 4 46.816 -7.765 -10.141 1 53.26 ? O31 3PH 302 A 1 
HETATM 30 C C31 3PH . . . F 4 47.866 -7.213 -9.475 1 49.55 ? C31 3PH 302 A 1 
HETATM 31 O O32 3PH . . . F 4 49.03 -7.259 -9.869 0.25 50.87 ? O32 3PH 302 A 1 
HETATM 32 C C32 3PH . . . F 4 47.504 -6.51 -8.165 1 42.48 ? C32 3PH 302 A 1 
HETATM 33 C C33 3PH . . . F 4 48.776 -5.977 -7.504 1 35.88 ? C33 3PH 302 A 1 
HETATM 34 C C34 3PH . . . F 4 48.452 -5.495 -6.088 0.92 31.68 ? C34 3PH 302 A 1 
HETATM 35 C C35 3PH . . . F 4 49.695 -4.853 -5.47 0.86 26.67 ? C35 3PH 302 A 1 
HETATM 36 C C36 3PH . . . F 4 49.438 -4.564 -3.99 0.51 21.74 ? C36 3PH 302 A 1 
HETATM 37 C C37 3PH . . . F 4 50.658 -4.984 -3.167 1 19.17 ? C37 3PH 302 A 1 
HETATM 38 C C38 3PH . . . F 4 50.216 -5.915 -2.037 0.38 21.45 ? C38 3PH 302 A 1 
HETATM 39 C C39 3PH . . . F 4 49.8 -5.083 -0.823 1 23.99 ? C39 3PH 302 A 1 
HETATM 40 C C3A 3PH . . . F 4 50.27 -5.777 0.457 0.71 26.24 ? C3A 3PH 302 A 1 
HETATM 41 C C3B 3PH . . . F 4 50.674 -4.723 1.49 1 27.77 ? C3B 3PH 302 A 1 
HETATM 42 C C3C 3PH . . . F 4 49.492 -3.788 1.755 0.96 27.86 ? C3C 3PH 302 A 1 
HETATM 43 C C3D 3PH . . . F 4 48.435 -3.98 0.666 0.61 25.61 ? C3D 3PH 302 A 1 
HETATM 44 C C3E 3PH . . . F 4 47.872 -2.618 0.255 0.37 23.58 ? C3E 3PH 302 A 1 
HETATM 45 C C3F 3PH . . . F 4 46.77 -2.205 1.232 0 22.23 ? C3F 3PH 302 A 1 
HETATM 46 C C3G 3PH . . . F 4 45.669 -1.459 0.474 0 21.07 ? C3G 3PH 302 A 1 
HETATM 47 C C3H 3PH . . . F 4 46.158 -0.054 0.117 0 20.68 ? C3H 3PH 302 A 1 
HETATM 48 C C3I 3PH . . . F 4 44.985 0.778 -0.404 0 20.68 ? C3I 3PH 302 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           48 
#