data_8YHQ # _model_server_result.job_id dhk9p--MdSSpbLa-rz6pPw _model_server_result.datetime_utc '2024-12-26 13:01:42' _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 8yhq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":401}' # _entry.id 8YHQ # _exptl.entry_id 8YHQ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 592.785 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate' _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 8YHQ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YHQ _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 eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA _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 ? 11 U N N ? 11 LA 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 disulf ? disulf1 E SG CYS 129 E CYS 159 1_555 E SG CYS 134 E CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? disulf ? disulf2 E SG CYS 148 E CYS 178 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? disulf ? disulf3 F SG CYS 29 F CYS 101 1_555 F SG CYS 51 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? disulf ? disulf4 N SG CYS 134 N CYS 164 1_555 N SG CYS 150 N CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? disulf ? disulf5 P SG CYS 29 O CYS 101 1_555 P SG CYS 51 O CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc6 G NE2 HIS 82 L HIS 82 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc7 G NE2 HIS 96 L HIS 96 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc8 G NE2 HIS 183 L HIS 183 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc9 G NE2 HIS 197 L HIS 197 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc10 M NE2 HIS 44 M HIS 105 1_555 KA FE HEM . M HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? # _chem_comp.formula 'C31 H61 O8 P' _chem_comp.formula_weight 592.785 _chem_comp.id 6PH _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate' _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 P O11 6PH sing 1 n n P O13 6PH sing 2 n n O11 C1 6PH sing 3 n n O12 P 6PH doub 4 n n O13 HO13 6PH sing 5 n n O14 P 6PH sing 6 n n O14 HO14 6PH sing 7 n n C1 H1 6PH sing 8 n n C1 H1A 6PH sing 9 n n C2 C1 6PH sing 10 n n C2 H2 6PH sing 11 n n C3 C2 6PH sing 12 n n C3 H3 6PH sing 13 n n C3 H3A 6PH sing 14 n n O31 C3 6PH sing 15 n n O32 C31 6PH doub 16 n n C31 O31 6PH sing 17 n n C32 C31 6PH sing 18 n n C32 H32 6PH sing 19 n n C32 H32A 6PH sing 20 n n C33 C32 6PH sing 21 n n C33 C34 6PH sing 22 n n C33 H33 6PH sing 23 n n C33 H33A 6PH sing 24 n n C34 C35 6PH sing 25 n n C34 H34 6PH sing 26 n n C34 H34A 6PH sing 27 n n C35 H35 6PH sing 28 n n C35 H35A 6PH sing 29 n n C36 C35 6PH sing 30 n n C36 C37 6PH sing 31 n n C36 H36 6PH sing 32 n n C36 H36A 6PH sing 33 n n C37 H37 6PH sing 34 n n C37 H37A 6PH sing 35 n n C38 C37 6PH sing 36 n n C38 C39 6PH sing 37 n n C38 H38 6PH sing 38 n n C38 H38A 6PH sing 39 n n C39 C3A 6PH sing 40 n n C39 H39 6PH sing 41 n n C39 H39A 6PH sing 42 n n C3A H3AA 6PH sing 43 n n C3A H3AB 6PH sing 44 n n C3B C3A 6PH sing 45 n n C3B C3C 6PH sing 46 n n C3B H3B 6PH sing 47 n n C3B H3BA 6PH sing 48 n n C3C C3D 6PH sing 49 n n C3C H3C 6PH sing 50 n n C3C H3CA 6PH sing 51 n n C3D H3D 6PH sing 52 n n C3D H3DA 6PH sing 53 n n C3D H3DB 6PH sing 54 n n O21 C2 6PH sing 55 n n O21 C21 6PH sing 56 n n C21 O22 6PH doub 57 n n C22 C21 6PH sing 58 n n C22 C23 6PH sing 59 n n C22 H22 6PH sing 60 n n C22 H22A 6PH sing 61 n n C23 H23 6PH sing 62 n n C23 H23A 6PH sing 63 n n C24 C23 6PH sing 64 n n C24 C25 6PH sing 65 n n C24 H24 6PH sing 66 n n C24 H24A 6PH sing 67 n n C25 H25 6PH sing 68 n n C25 H25A 6PH sing 69 n n C26 C25 6PH sing 70 n n C26 H26 6PH sing 71 n n C26 H26A 6PH sing 72 n n C27 C26 6PH sing 73 n n C27 H27 6PH sing 74 n n C27 H27A 6PH sing 75 n n C28 C27 6PH sing 76 n n C28 H28 6PH sing 77 n n C28 H28A 6PH sing 78 n n C29 C28 6PH sing 79 n n C29 H29 6PH sing 80 n n C29 H29A 6PH sing 81 n n C2A C29 6PH sing 82 n n C2A C2B 6PH sing 83 n n C2A H2A 6PH sing 84 n n C2A H2AA 6PH sing 85 n n C2B C2C 6PH sing 86 n n C2B H2B 6PH sing 87 n n C2C C2D 6PH sing 88 n n C2C H2C 6PH sing 89 n n C2D C2E 6PH sing 90 n n C2D H2D 6PH sing 91 n n C2D H2DA 6PH sing 92 n n C2E C2F 6PH sing 93 n n C2E H2E 6PH sing 94 n n C2F H2F 6PH sing 95 n n C2F H2FA 6PH sing 96 n n C2B H58 6PH sing 97 n n C2C H59 6PH sing 98 n n C2E H60 6PH sing 99 n n C2F H61 6PH sing 100 n n # _atom_sites.entry_id 8YHQ _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 U 11 6PH C 1 401 402 6PH 6PH . V 12 9PE C 1 402 403 9PE 9PE . W 13 HEM C 1 403 404 HEM HEM . X 13 HEM C 1 404 405 HEM HEM . Y 14 8PE C 1 405 406 8PE 8PE . Z 15 CN5 C 1 406 407 CN5 CN5 . AA 16 UQ6 C 1 407 408 UQ6 UQ6 . BA 17 A1D6K C 1 408 401 A1D6K A1D . CA 13 HEM D 1 401 402 HEM HEM . DA 18 7PH D 1 402 401 7PH 7PH . EA 16 UQ6 L 1 401 402 UQ6 UQ6 . FA 12 9PE L 1 402 403 9PE 9PE . GA 13 HEM L 1 403 404 HEM HEM . HA 19 CN3 L 1 404 405 CN3 CN3 . IA 13 HEM L 1 405 406 HEM HEM . JA 17 A1D6K L 1 406 401 A1D6K A1D . KA 13 HEM M 1 401 401 HEM HEM . LA 11 6PH N 1 401 401 6PH 6PH . MA 18 7PH N 1 402 402 7PH 7PH . NA 14 8PE Q 1 101 101 8PE 8PE . # 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 P P 6PH . . . LA 11 134.967 166.123 132.342 1 36.4 ? P 6PH 401 N 1 HETATM 2 O O11 6PH . . . LA 11 135.161 165.401 130.876 1 36.4 ? O11 6PH 401 N 1 HETATM 3 O O12 6PH . . . LA 11 135.368 165.148 133.423 1 36.4 ? O12 6PH 401 N 1 HETATM 4 O O13 6PH . . . LA 11 135.838 167.352 132.425 1 36.4 ? O13 6PH 401 N 1 HETATM 5 O O14 6PH . . . LA 11 133.517 166.506 132.519 1 36.4 ? O14 6PH 401 N 1 HETATM 6 C C1 6PH . . . LA 11 134.655 164.104 130.768 1 36.4 ? C1 6PH 401 N 1 HETATM 7 C C2 6PH . . . LA 11 135.661 162.945 130.691 1 36.4 ? C2 6PH 401 N 1 HETATM 8 C C3 6PH . . . LA 11 137.137 163.388 130.651 1 36.4 ? C3 6PH 401 N 1 HETATM 9 O O31 6PH . . . LA 11 137.748 162.893 129.498 1 36.4 ? O31 6PH 401 N 1 HETATM 10 O O32 6PH . . . LA 11 136.748 164.492 128.239 1 36.4 ? O32 6PH 401 N 1 HETATM 11 C C31 6PH . . . LA 11 137.316 163.453 128.29 1 36.4 ? C31 6PH 401 N 1 HETATM 12 C C32 6PH . . . LA 11 137.585 162.667 127.027 1 36.4 ? C32 6PH 401 N 1 HETATM 13 C C33 6PH . . . LA 11 139.086 162.76 126.782 1 36.4 ? C33 6PH 401 N 1 HETATM 14 C C34 6PH . . . LA 11 139.647 161.896 125.649 1 36.4 ? C34 6PH 401 N 1 HETATM 15 C C35 6PH . . . LA 11 138.672 161.374 124.584 1 36.4 ? C35 6PH 401 N 1 HETATM 16 C C36 6PH . . . LA 11 138.279 159.91 124.798 1 36.4 ? C36 6PH 401 N 1 HETATM 17 C C37 6PH . . . LA 11 138.602 159.077 123.559 1 36.4 ? C37 6PH 401 N 1 HETATM 18 C C38 6PH . . . LA 11 140.107 158.893 123.358 1 36.4 ? C38 6PH 401 N 1 HETATM 19 C C39 6PH . . . LA 11 140.375 158.342 121.96 1 36.4 ? C39 6PH 401 N 1 HETATM 20 C C3A 6PH . . . LA 11 139.917 156.897 121.849 1 36.4 ? C3A 6PH 401 N 1 HETATM 21 C C3B 6PH . . . LA 11 140.797 156.169 120.839 1 36.4 ? C3B 6PH 401 N 1 HETATM 22 C C3C 6PH . . . LA 11 140.402 154.697 120.76 1 36.4 ? C3C 6PH 401 N 1 HETATM 23 C C3D 6PH . . . LA 11 141.109 153.921 121.864 1 36.4 ? C3D 6PH 401 N 1 HETATM 24 O O21 6PH . . . LA 11 135.439 162.087 131.786 1 36.4 ? O21 6PH 401 N 1 HETATM 25 O O22 6PH . . . LA 11 136.653 160.578 132.86 1 36.4 ? O22 6PH 401 N 1 HETATM 26 C C21 6PH . . . LA 11 136.111 160.846 131.843 1 36.4 ? C21 6PH 401 N 1 HETATM 27 C C22 6PH . . . LA 11 136.139 159.876 130.647 1 36.4 ? C22 6PH 401 N 1 HETATM 28 C C23 6PH . . . LA 11 137.08 158.669 130.811 1 36.4 ? C23 6PH 401 N 1 HETATM 29 C C24 6PH . . . LA 11 138.176 158.569 129.739 1 36.4 ? C24 6PH 401 N 1 HETATM 30 C C25 6PH . . . LA 11 137.816 157.539 128.667 1 36.4 ? C25 6PH 401 N 1 HETATM 31 C C26 6PH . . . LA 11 139.023 157.226 127.783 1 36.4 ? C26 6PH 401 N 1 HETATM 32 C C27 6PH . . . LA 11 138.73 155.953 126.993 1 36.4 ? C27 6PH 401 N 1 HETATM 33 C C28 6PH . . . LA 11 139.792 155.753 125.908 1 36.4 ? C28 6PH 401 N 1 HETATM 34 C C29 6PH . . . LA 11 140.251 154.294 125.766 1 36.4 ? C29 6PH 401 N 1 HETATM 35 C C2A 6PH . . . LA 11 141.753 154.089 126.014 1 36.4 ? C2A 6PH 401 N 1 HETATM 36 C C2B 6PH . . . LA 11 141.898 152.872 126.906 1 36.4 ? C2B 6PH 401 N 1 HETATM 37 C C2C 6PH . . . LA 11 143.356 152.433 127.033 1 36.4 ? C2C 6PH 401 N 1 HETATM 38 C C2D 6PH . . . LA 11 143.468 151.368 128.124 1 36.4 ? C2D 6PH 401 N 1 HETATM 39 C C2E 6PH . . . LA 11 142.862 150.039 127.672 1 36.4 ? C2E 6PH 401 N 1 HETATM 40 C C2F 6PH . . . LA 11 142.459 149.207 128.883 1 36.4 ? C2F 6PH 401 N 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 84 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #