data_1PUB # _model_server_result.job_id wPrQuvLBYbS2msIts1WSlw _model_server_result.datetime_utc '2024-11-29 12:49:19' _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 1pub # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2341}' # _entry.id 1PUB # _exptl.entry_id 1PUB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 704.998 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE _entity.pdbx_number_of_molecules 1 _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 1PUB _cell.length_a 40.07 _cell.length_b 42.42 _cell.length_c 113.78 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PUB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 x,y,z _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A SG CYS 8 A CYS 8 1_555 A SG CYS 152 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf2 A SG CYS 68 A CYS 68 1_555 A SG CYS 75 A CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 81 A CYS 81 1_555 A SG CYS 107 A CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 94 A CYS 94 1_555 A SG CYS 105 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _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 1PUB _atom_sites.fract_transf_matrix[1][1] 0.024956 _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] 0.023574 _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] 0.008789 _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 B 2 3PH A 1 2341 2341 3PH PA . C 3 HOH A 1 2342 1 HOH TIP . C 3 HOH A 2 2343 2 HOH TIP . C 3 HOH A 3 2344 3 HOH TIP . C 3 HOH A 4 2345 4 HOH TIP . C 3 HOH A 5 2346 5 HOH TIP . C 3 HOH A 6 2347 6 HOH TIP . C 3 HOH A 7 2348 7 HOH TIP . C 3 HOH A 8 2349 8 HOH TIP . C 3 HOH A 9 2350 9 HOH TIP . C 3 HOH A 10 2351 10 HOH TIP . C 3 HOH A 11 2352 11 HOH TIP . C 3 HOH A 12 2353 12 HOH TIP . C 3 HOH A 13 2354 13 HOH TIP . C 3 HOH A 14 2355 14 HOH TIP . C 3 HOH A 15 2356 15 HOH TIP . C 3 HOH A 16 2357 16 HOH TIP . C 3 HOH A 17 2358 17 HOH TIP . C 3 HOH A 18 2359 18 HOH TIP . C 3 HOH A 19 2360 19 HOH TIP . C 3 HOH A 20 2361 20 HOH TIP . C 3 HOH A 21 2362 21 HOH TIP . C 3 HOH A 22 2363 22 HOH TIP . C 3 HOH A 23 2364 23 HOH TIP . C 3 HOH A 24 2365 24 HOH TIP . C 3 HOH A 25 2366 25 HOH TIP . C 3 HOH A 26 2367 26 HOH TIP . C 3 HOH A 27 2368 27 HOH TIP . C 3 HOH A 28 2369 28 HOH TIP . C 3 HOH A 29 2370 29 HOH TIP . C 3 HOH A 30 2371 30 HOH TIP . C 3 HOH A 31 2372 31 HOH TIP . C 3 HOH A 32 2373 32 HOH TIP . C 3 HOH A 33 2374 33 HOH TIP . C 3 HOH A 34 2375 34 HOH TIP . C 3 HOH A 35 2376 35 HOH TIP . C 3 HOH A 36 2377 36 HOH TIP . C 3 HOH A 37 2378 37 HOH TIP . C 3 HOH A 38 2379 38 HOH TIP . C 3 HOH A 39 2380 39 HOH TIP . C 3 HOH A 40 2381 40 HOH TIP . C 3 HOH A 41 2382 41 HOH TIP . C 3 HOH A 42 2383 42 HOH TIP . C 3 HOH A 43 2384 43 HOH TIP . C 3 HOH A 44 2385 44 HOH TIP . C 3 HOH A 45 2386 45 HOH TIP . C 3 HOH A 46 2387 46 HOH TIP . C 3 HOH A 47 2388 47 HOH TIP . C 3 HOH A 48 2389 48 HOH TIP . C 3 HOH A 49 2390 49 HOH TIP . C 3 HOH A 50 2391 50 HOH TIP . C 3 HOH A 51 2392 51 HOH TIP . C 3 HOH A 52 2393 52 HOH TIP . C 3 HOH A 53 2394 53 HOH TIP . C 3 HOH A 54 2395 54 HOH TIP . C 3 HOH A 55 2396 55 HOH TIP . C 3 HOH A 56 2397 56 HOH TIP . C 3 HOH A 57 2398 57 HOH TIP . C 3 HOH A 58 2399 58 HOH TIP . C 3 HOH A 59 2400 59 HOH TIP . C 3 HOH A 60 2401 60 HOH TIP . C 3 HOH A 61 2402 61 HOH TIP . # 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 . . . B 2 23.976 -7.623 3.76 0.7 81.15 ? O13 3PH 2341 A 1 HETATM 2 P P 3PH . . . B 2 25.232 -6.742 3.922 0.7 81.15 ? P 3PH 2341 A 1 HETATM 3 O O14 3PH . . . B 2 25.186 -5.608 2.887 0.7 79.93 ? O14 3PH 2341 A 1 HETATM 4 O O12 3PH . . . B 2 26.478 -7.603 3.66 0.7 81.15 ? O12 3PH 2341 A 1 HETATM 5 O O11 3PH . . . B 2 25.283 -6.153 5.379 0.7 81.15 ? O11 3PH 2341 A 1 HETATM 6 C C1 3PH . . . B 2 26.518 -5.377 5.647 0.7 81.15 ? C1 3PH 2341 A 1 HETATM 7 C C2 3PH . . . B 2 27.034 -5.564 7.084 0.7 81.15 ? C2 3PH 2341 A 1 HETATM 8 O O21 3PH . . . B 2 26.56 -6.905 7.585 0.7 81.15 ? O21 3PH 2341 A 1 HETATM 9 C C21 3PH . . . B 2 27.045 -7.602 8.859 0.7 81.15 ? C21 3PH 2341 A 1 HETATM 10 O O22 3PH . . . B 2 26.575 -8.731 9.167 0.7 81.15 ? O22 3PH 2341 A 1 HETATM 11 C C22 3PH . . . B 2 28.109 -6.942 9.772 0.7 80.91 ? C22 3PH 2341 A 1 HETATM 12 C C23 3PH . . . B 2 28.26 -7.62 11.154 0.7 76.32 ? C23 3PH 2341 A 1 HETATM 13 C C24 3PH . . . B 2 27.816 -6.728 12.322 0.7 69.84 ? C24 3PH 2341 A 1 HETATM 14 C C25 3PH . . . B 2 27.092 -7.524 13.416 0.7 66.16 ? C25 3PH 2341 A 1 HETATM 15 C C26 3PH . . . B 2 28.021 -7.976 14.554 0.7 55.82 ? C26 3PH 2341 A 1 HETATM 16 C C27 3PH . . . B 2 27.252 -8.131 15.862 0.7 56.84 ? C27 3PH 2341 A 1 HETATM 17 C C28 3PH . . . B 2 28.143 -8.581 17.002 0.7 59.21 ? C28 3PH 2341 A 1 HETATM 18 C C29 3PH . . . B 2 27.741 -7.907 18.307 0.7 62.12 ? C29 3PH 2341 A 1 HETATM 19 C C2A 3PH . . . B 2 27.71 -8.891 19.482 0.7 62.42 ? C2A 3PH 2341 A 1 HETATM 20 C C2B 3PH . . . B 2 27.201 -8.237 20.777 0.7 60.83 ? C2B 3PH 2341 A 1 HETATM 21 C C2C 3PH . . . B 2 26.094 -9.053 21.46 0.7 50.77 ? C2C 3PH 2341 A 1 HETATM 22 C C2D 3PH . . . B 2 25.106 -8.165 22.223 0.7 43.17 ? C2D 3PH 2341 A 1 HETATM 23 C C2E 3PH . . . B 2 25.39 -8.167 23.726 0.7 34.78 ? C2E 3PH 2341 A 1 HETATM 24 C C2F 3PH . . . B 2 25.668 -6.771 24.268 0.7 33.52 ? C2F 3PH 2341 A 1 HETATM 25 C C2G 3PH . . . B 2 27.092 -6.635 24.847 0.7 44.43 ? C2G 3PH 2341 A 1 HETATM 26 C C2H 3PH . . . B 2 27.245 -5.395 25.771 0.7 41.44 ? C2H 3PH 2341 A 1 HETATM 27 C C2I 3PH . . . B 2 28.483 -5.4 26.662 0.7 27.1 ? C2I 3PH 2341 A 1 HETATM 28 C C3 3PH . . . B 2 26.672 -4.414 8.041 0.7 81.15 ? C3 3PH 2341 A 1 HETATM 29 O O31 3PH . . . B 2 25.886 -3.361 7.404 0.7 81.15 ? O31 3PH 2341 A 1 HETATM 30 C C31 3PH . . . B 2 25.516 -2.211 8.274 0.7 77.85 ? C31 3PH 2341 A 1 HETATM 31 O O32 3PH . . . B 2 24.843 -1.27 7.812 0.7 77.36 ? O32 3PH 2341 A 1 HETATM 32 C C32 3PH . . . B 2 26.002 -2.222 9.753 0.7 70.87 ? C32 3PH 2341 A 1 HETATM 33 C C33 3PH . . . B 2 24.982 -2.663 10.816 0.7 65.11 ? C33 3PH 2341 A 1 HETATM 34 C C34 3PH . . . B 2 25.212 -1.951 12.149 0.7 59.87 ? C34 3PH 2341 A 1 HETATM 35 C C35 3PH . . . B 2 25.438 -2.892 13.301 0.7 47.51 ? C35 3PH 2341 A 1 HETATM 36 C C36 3PH . . . B 2 26.071 -2.158 14.474 0.7 45.43 ? C36 3PH 2341 A 1 HETATM 37 C C37 3PH . . . B 2 26.307 -3.097 15.661 0.7 52.49 ? C37 3PH 2341 A 1 HETATM 38 C C38 3PH . . . B 2 27.647 -2.836 16.385 0.7 54.92 ? C38 3PH 2341 A 1 HETATM 39 C C39 3PH . . . B 2 27.469 -2.236 17.794 0.7 49.42 ? C39 3PH 2341 A 1 HETATM 40 C C3A 3PH . . . B 2 27.075 -3.288 18.834 0.7 49.6 ? C3A 3PH 2341 A 1 HETATM 41 C C3B 3PH . . . B 2 28.285 -3.843 19.56 0.7 50.98 ? C3B 3PH 2341 A 1 HETATM 42 C C3C 3PH . . . B 2 28.723 -2.911 20.668 0.7 58.53 ? C3C 3PH 2341 A 1 HETATM 43 C C3D 3PH . . . B 2 30.161 -3.157 21.099 0.7 61.6 ? C3D 3PH 2341 A 1 HETATM 44 C C3E 3PH . . . B 2 30.57 -2.191 22.214 0.7 64.76 ? C3E 3PH 2341 A 1 HETATM 45 C C3F 3PH . . . B 2 31.581 -2.797 23.181 0.7 64.43 ? C3F 3PH 2341 A 1 HETATM 46 C C3G 3PH . . . B 2 33.003 -2.327 22.9 0.7 56.32 ? C3G 3PH 2341 A 1 HETATM 47 C C3H 3PH . . . B 2 34.035 -3.242 23.568 0.7 50.31 ? C3H 3PH 2341 A 1 HETATM 48 C C3I 3PH . . . B 2 34.316 -4.535 22.813 0.7 51.18 ? C3I 3PH 2341 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 48 #