data_6E1M # _model_server_result.job_id KasAowFxd1jcWfpIdH_NKA _model_server_result.datetime_utc '2025-01-11 19:03:08' _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 6e1m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":813}' # _entry.id 6E1M # _exptl.entry_id 6E1M _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.entry_id 6E1M _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E1M _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 O N N ? 4 Y 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 covale ? covale1 A C SEP 12 A SEP 22 1_555 A N GLU 13 A GLU 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C ILE 15 A ILE 25 1_555 A N TPO 16 A TPO 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 A C TPO 16 A TPO 26 1_555 A N HIS 17 A HIS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C GLY 18 A GLY 28 1_555 A N TPO 19 A TPO 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C TPO 19 A TPO 29 1_555 A N PRO 20 A PRO 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.358 ? covale ? covale6 B C SEP 12 B SEP 22 1_555 B N GLU 13 B GLU 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 B C ILE 15 B ILE 25 1_555 B N TPO 16 B TPO 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 B C TPO 16 B TPO 26 1_555 B N HIS 17 B HIS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale9 B C GLY 18 B GLY 28 1_555 B N TPO 19 B TPO 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 B C TPO 19 B TPO 29 1_555 B N PRO 20 B PRO 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? metalc ? metalc1 A OD1 ASP 325 A ASP 335 1_555 G CA CA . A CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc2 A OD1 ASN 329 A ASN 339 1_555 G CA CA . A CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc3 A O GLU 331 A GLU 341 1_555 G CA CA . A CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc4 A OE2 GLU 364 A GLU 374 1_555 F CA CA . A CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc5 B OD1 ASP 327 B ASP 337 1_555 Q CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.015 ? metalc ? metalc6 B OD2 ASP 327 B ASP 337 1_555 Q CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc7 B OD1 ASN 329 B ASN 339 1_555 Q CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc8 B O GLU 331 B GLU 341 1_555 Q CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc9 B OE1 GLU 364 B GLU 374 1_555 P CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc10 B OE2 GLU 364 B GLU 374 1_555 P CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? # _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 6E1M _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 C 2 CA A 1 801 802 CA CA . D 2 CA A 1 802 803 CA CA . E 2 CA A 1 803 804 CA CA . F 2 CA A 1 804 805 CA CA . G 2 CA A 1 805 806 CA CA . H 3 PLM A 1 806 901 PLM PLM . I 3 PLM A 1 807 902 PLM PLM . J 3 PLM A 1 808 903 PLM PLM . K 3 PLM A 1 809 904 PLM PLM . L 3 PLM A 1 810 905 PLM PLM . M 3 PLM A 1 811 906 PLM PLM . N 3 PLM A 1 812 907 PLM PLM . O 4 3PH A 1 813 920 3PH 6PH . P 2 CA B 1 801 805 CA CA . Q 2 CA B 1 802 806 CA CA . R 3 PLM B 1 803 901 PLM PLM . S 3 PLM B 1 804 902 PLM PLM . T 3 PLM B 1 805 903 PLM PLM . U 3 PLM B 1 806 904 PLM PLM . V 3 PLM B 1 807 905 PLM PLM . W 3 PLM B 1 808 906 PLM PLM . X 3 PLM B 1 809 907 PLM PLM . Y 4 3PH B 1 810 920 3PH 6PH . Z 5 HOH A 1 901 1 HOH HOH . AA 5 HOH B 1 901 2 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 . . . O 4 184.297 154.57 159.191 1 94.11 ? O13 3PH 813 A 1 HETATM 2 P P 3PH . . . O 4 183.764 153.277 158.631 1 94.11 ? P 3PH 813 A 1 HETATM 3 O O14 3PH . . . O 4 184.555 152.13 159.209 1 94.11 ? O14 3PH 813 A 1 HETATM 4 O O12 3PH . . . O 4 183.934 153.283 157.133 1 94.11 ? O12 3PH 813 A 1 HETATM 5 O O11 3PH . . . O 4 182.162 153.13 159.02 1 94.11 ? O11 3PH 813 A 1 HETATM 6 C C1 3PH . . . O 4 181.192 153.503 158.07 1 94.11 ? C1 3PH 813 A 1 HETATM 7 C C2 3PH . . . O 4 180.81 152.259 157.254 1 94.11 ? C2 3PH 813 A 1 HETATM 8 O O21 3PH . . . O 4 179.567 152.487 156.588 1 94.11 ? O21 3PH 813 A 1 HETATM 9 C C21 3PH . . . O 4 179.652 152.604 155.192 1 94.11 ? C21 3PH 813 A 1 HETATM 10 O O22 3PH . . . O 4 179.73 153.662 154.662 1 94.11 ? O22 3PH 813 A 1 HETATM 11 C C22 3PH . . . O 4 179.674 151.349 154.313 1 94.11 ? C22 3PH 813 A 1 HETATM 12 C C23 3PH . . . O 4 178.483 150.379 154.487 1 94.11 ? C23 3PH 813 A 1 HETATM 13 C C24 3PH . . . O 4 178.427 149.269 153.383 1 94.11 ? C24 3PH 813 A 1 HETATM 14 C C25 3PH . . . O 4 179.635 149.253 152.405 1 94.11 ? C25 3PH 813 A 1 HETATM 15 C C26 3PH . . . O 4 179.412 148.425 151.131 1 94.11 ? C26 3PH 813 A 1 HETATM 16 C C27 3PH . . . O 4 177.989 148.562 150.585 1 94.11 ? C27 3PH 813 A 1 HETATM 17 C C28 3PH . . . O 4 177.964 149.429 149.333 1 94.11 ? C28 3PH 813 A 1 HETATM 18 C C29 3PH . . . O 4 178.605 148.729 148.148 1 94.11 ? C29 3PH 813 A 1 HETATM 19 C C2A 3PH . . . O 4 177.605 148.621 147.006 1 94.11 ? C2A 3PH 813 A 1 HETATM 20 C C2B 3PH . . . O 4 177.698 149.808 146.068 1 94.11 ? C2B 3PH 813 A 1 HETATM 21 C C2C 3PH . . . O 4 176.387 150.576 145.982 1 94.11 ? C2C 3PH 813 A 1 HETATM 22 C C2D 3PH . . . O 4 176.211 151.269 144.643 1 94.11 ? C2D 3PH 813 A 1 HETATM 23 C C2E 3PH . . . O 4 174.875 151.997 144.584 1 94.11 ? C2E 3PH 813 A 1 HETATM 24 C C2F 3PH . . . O 4 175.093 153.5 144.429 1 94.11 ? C2F 3PH 813 A 1 HETATM 25 C C2G 3PH . . . O 4 174.423 154.322 145.543 1 94.11 ? C2G 3PH 813 A 1 HETATM 26 C C2H 3PH . . . O 4 174.994 155.744 145.663 1 94.11 ? C2H 3PH 813 A 1 HETATM 27 C C2I 3PH . . . O 4 173.92 156.777 146.019 1 94.11 ? C2I 3PH 813 A 1 HETATM 28 C C3 3PH . . . O 4 180.727 151.001 158.137 1 94.11 ? C3 3PH 813 A 1 HETATM 29 O O31 3PH . . . O 4 180.647 149.87 157.307 1 94.11 ? O31 3PH 813 A 1 HETATM 30 C C31 3PH . . . O 4 180.766 148.646 157.986 1 94.11 ? C31 3PH 813 A 1 HETATM 31 O O32 3PH . . . O 4 180.054 148.415 158.902 1 94.11 ? O32 3PH 813 A 1 HETATM 32 C C32 3PH . . . O 4 181.811 147.602 157.555 1 94.11 ? C32 3PH 813 A 1 HETATM 33 C C33 3PH . . . O 4 181.331 146.452 156.627 1 94.11 ? C33 3PH 813 A 1 HETATM 34 C C34 3PH . . . O 4 181.032 146.747 155.115 1 94.11 ? C34 3PH 813 A 1 HETATM 35 C C35 3PH . . . O 4 182.192 147.131 154.133 1 94.11 ? C35 3PH 813 A 1 HETATM 36 C C36 3PH . . . O 4 183.379 148.14 154.403 1 94.11 ? C36 3PH 813 A 1 HETATM 37 C C37 3PH . . . O 4 183.194 149.302 153.396 1 94.11 ? C37 3PH 813 A 1 HETATM 38 C C38 3PH . . . O 4 183.855 150.675 153.684 1 94.11 ? C38 3PH 813 A 1 HETATM 39 C C39 3PH . . . O 4 183.86 151.579 152.421 1 94.11 ? C39 3PH 813 A 1 HETATM 40 C C3A 3PH . . . O 4 182.697 151.32 151.463 1 94.11 ? C3A 3PH 813 A 1 HETATM 41 C C3B 3PH . . . O 4 182.233 152.591 150.733 1 94.11 ? C3B 3PH 813 A 1 HETATM 42 C C3C 3PH . . . O 4 181.12 152.308 149.734 1 94.11 ? C3C 3PH 813 A 1 HETATM 43 C C3D 3PH . . . O 4 181.191 153.354 148.602 1 94.11 ? C3D 3PH 813 A 1 HETATM 44 C C3E 3PH . . . O 4 180.213 153.115 147.453 1 94.11 ? C3E 3PH 813 A 1 HETATM 45 C C3F 3PH . . . O 4 180.955 153.207 146.104 1 94.11 ? C3F 3PH 813 A 1 HETATM 46 C C3G 3PH . . . O 4 180.065 152.845 144.92 1 94.11 ? C3G 3PH 813 A 1 HETATM 47 C C3H 3PH . . . O 4 180.841 152.048 143.864 1 94.11 ? C3H 3PH 813 A 1 HETATM 48 C C3I 3PH . . . O 4 179.988 151.736 142.63 1 94.11 ? C3I 3PH 813 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 418 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 48 #