data_3TH1 # _model_server_result.job_id 5_Y9IkjJp75rdZPADi_HFQ _model_server_result.datetime_utc '2025-02-28 13:29:47' _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":"M","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 . . . M 4 30.523 -21.538 -5.448 0.91 33.94 1 O13 3PH 302 B 1 HETATM 2 P P 3PH . . . M 4 29.764 -20.325 -5.825 0.91 77.91 ? P 3PH 302 B 1 HETATM 3 O O14 3PH . . . M 4 30.711 -19.087 -6.259 0.91 78.17 ? O14 3PH 302 B 1 HETATM 4 O O12 3PH . . . M 4 28.764 -20.56 -7.075 0.91 141 ? O12 3PH 302 B 1 HETATM 5 O O11 3PH . . . M 4 28.833 -19.756 -4.631 0.91 75.19 ? O11 3PH 302 B 1 HETATM 6 C C1 3PH . . . M 4 27.41 -19.759 -4.77 0.91 75.23 ? C1 3PH 302 B 1 HETATM 7 C C2 3PH . . . M 4 26.844 -21.062 -4.203 0 74.02 ? C2 3PH 302 B 1 HETATM 8 O O21 3PH . . . M 4 26.387 -20.843 -2.866 0.91 76.03 ? O21 3PH 302 B 1 HETATM 9 C C21 3PH . . . M 4 25.67 -19.688 -2.815 0.91 75.49 ? C21 3PH 302 B 1 HETATM 10 O O22 3PH . . . M 4 26.172 -18.566 -2.824 0.91 76.06 ? O22 3PH 302 B 1 HETATM 11 C C22 3PH . . . M 4 24.153 -19.872 -2.743 0.91 73.5 ? C22 3PH 302 B 1 HETATM 12 C C23 3PH . . . M 4 23.832 -21.228 -2.11 0.91 70.92 ? C23 3PH 302 B 1 HETATM 13 C C24 3PH . . . M 4 24.492 -22.341 -2.925 0.91 67.05 ? C24 3PH 302 B 1 HETATM 14 C C25 3PH . . . M 4 24.213 -23.693 -2.263 0.91 61.65 ? C25 3PH 302 B 1 HETATM 15 C C26 3PH . . . M 4 24.277 -24.8 -3.317 0.91 55.84 ? C26 3PH 302 B 1 HETATM 16 C C27 3PH . . . M 4 24.57 -26.138 -2.635 0.91 52.4 ? C27 3PH 302 B 1 HETATM 17 C C28 3PH . . . M 4 23.795 -27.252 -3.34 0.91 50.53 ? C28 3PH 302 B 1 HETATM 18 C C29 3PH . . . M 4 24.571 -27.711 -4.576 0.91 48.7 ? C29 3PH 302 B 1 HETATM 19 C C2A 3PH . . . M 4 23.691 -27.56 -5.818 0.91 47.92 ? C2A 3PH 302 B 1 HETATM 20 C C2B 3PH . . . M 4 23.739 -28.851 -6.638 0.91 47.3 ? C2B 3PH 302 B 1 HETATM 21 C C2C 3PH . . . M 4 23.387 -28.544 -8.095 0.91 45.68 ? C2C 3PH 302 B 1 HETATM 22 C C2D 3PH . . . M 4 22.836 -29.805 -8.764 0.91 43.11 ? C2D 3PH 302 B 1 HETATM 23 C C2E 3PH . . . M 4 23.637 -30.102 -10.033 0.91 42.28 ? C2E 3PH 302 B 1 HETATM 24 C C2F 3PH . . . M 4 24.693 -31.167 -9.732 0.91 41.01 ? C2F 3PH 302 B 1 HETATM 25 C C2G 3PH . . . M 4 25.436 -31.529 -11.02 0.91 38.91 ? C2G 3PH 302 B 1 HETATM 26 C C2H 3PH . . . M 4 25.492 -33.05 -11.167 0.91 36.98 ? C2H 3PH 302 B 1 HETATM 27 C C2I 3PH . . . M 4 26.932 -33.483 -11.45 0.91 37.1 ? C2I 3PH 302 B 1 HETATM 28 C C3 3PH . . . M 4 27.935 -22.135 -4.201 0.91 69.05 ? C3 3PH 302 B 1 HETATM 29 O O31 3PH . . . M 4 28.032 -22.72 -5.502 0.91 63.12 ? O31 3PH 302 B 1 HETATM 30 C C31 3PH . . . M 4 27.023 -23.615 -5.674 0.91 57.12 ? C31 3PH 302 B 1 HETATM 31 O O32 3PH . . . M 4 25.906 -23.498 -5.171 0.91 57.75 ? O32 3PH 302 B 1 HETATM 32 C C32 3PH . . . M 4 27.367 -24.817 -6.556 0.91 50.1 ? C32 3PH 302 B 1 HETATM 33 C C33 3PH . . . M 4 27.993 -25.918 -5.698 0.91 44.3 ? C33 3PH 302 B 1 HETATM 34 C C34 3PH . . . M 4 27.985 -27.237 -6.473 0.91 40.04 ? C34 3PH 302 B 1 HETATM 35 C C35 3PH . . . M 4 28.063 -26.948 -7.973 0.91 38.11 ? C35 3PH 302 B 1 HETATM 36 C C36 3PH . . . M 4 28.449 -28.226 -8.721 0.91 35.62 ? C36 3PH 302 B 1 HETATM 37 C C37 3PH . . . M 4 28.14 -29.442 -7.845 0.91 31.75 ? C37 3PH 302 B 1 HETATM 38 C C38 3PH . . . M 4 28.636 -30.711 -8.541 0.91 28.15 ? C38 3PH 302 B 1 HETATM 39 C C39 3PH . . . M 4 30.166 -30.709 -8.578 0.91 25.32 ? C39 3PH 302 B 1 HETATM 40 C C3A 3PH . . . M 4 30.677 -32.149 -8.653 0.91 24.94 ? C3A 3PH 302 B 1 HETATM 41 C C3B 3PH . . . M 4 32.011 -32.179 -9.401 0.91 26.09 ? C3B 3PH 302 B 1 HETATM 42 C C3C 3PH . . . M 4 32.474 -33.629 -9.563 0.91 26.73 ? C3C 3PH 302 B 1 HETATM 43 C C3D 3PH . . . M 4 32.506 -33.992 -11.049 0.91 29.34 ? C3D 3PH 302 B 1 HETATM 44 C C3E 3PH . . . M 4 32.304 -32.728 -11.888 0.91 33.47 ? C3E 3PH 302 B 1 HETATM 45 C C3F 3PH . . . M 4 31.836 -33.117 -13.292 0.91 37.13 ? C3F 3PH 302 B 1 HETATM 46 C C3G 3PH . . . M 4 30.435 -32.554 -13.537 0.91 39.25 ? C3G 3PH 302 B 1 HETATM 47 C C3H 3PH . . . M 4 30.461 -31.634 -14.76 0.91 40.62 ? C3H 3PH 302 B 1 HETATM 48 C C3I 3PH . . . M 4 29.09 -31.645 -15.437 0.91 40.8 ? C3I 3PH 302 B 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 48 #