data_2AT9 # _model_server_result.job_id pFx2r44sYKLFLot6mz2zIw _model_server_result.datetime_utc '2024-12-26 15:24:33' _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 2at9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":269}' # _entry.id 2AT9 # _exptl.entry_id 2AT9 _exptl.method 'ELECTRON CRYSTALLOGRAPHY' # _entity.details ? _entity.formula_weight 901.222 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-[[3-METHYLPHOSPHONO-GLYCEROLYL]PHOSPHONYL]-[1,2-DI[2,6,10,14-TETRAMETHYL-HEXADECAN-16-YL]GLYCEROL _entity.pdbx_number_of_molecules 8 _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 2AT9 _cell.length_a 62.45 _cell.length_b 62.45 _cell.length_c 100 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2AT9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 216 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 249 _struct_conn.ptnr2_symmetry 1_555 _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 A _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 1.343 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C47 H98 O11 P2' _chem_comp.formula_weight 901.222 _chem_comp.id 2DP _chem_comp.mon_nstd_flag . _chem_comp.name 3-[[3-METHYLPHOSPHONO-GLYCEROLYL]PHOSPHONYL]-[1,2-DI[2,6,10,14-TETRAMETHYL-HEXADECAN-16-YL]GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 C2 2DP sing 1 n n C1 O1 2DP sing 2 n n C1 H11 2DP sing 3 n n C1 H12 2DP sing 4 n n C2 C3 2DP sing 5 n n C2 O2 2DP sing 6 n n C2 H2 2DP sing 7 n n C3 O3 2DP sing 8 n n C3 H31 2DP sing 9 n n C3 H32 2DP sing 10 n n C4 C5 2DP sing 11 n n C4 O6 2DP sing 12 n n C4 H41 2DP sing 13 n n C4 H42 2DP sing 14 n n C5 C6 2DP sing 15 n n C5 O7 2DP sing 16 n n C5 H5 2DP sing 17 n n C6 O8 2DP sing 18 n n C6 H61 2DP sing 19 n n C6 H62 2DP sing 20 n n C11 C12 2DP sing 21 n n C11 O1 2DP sing 22 n n C11 H111 2DP sing 23 n n C11 H112 2DP sing 24 n n C12 C13 2DP sing 25 n n C12 H121 2DP sing 26 n n C12 H122 2DP sing 27 n n C13 C14 2DP sing 28 n n C13 C15 2DP sing 29 n n C13 H13 2DP sing 30 n n C14 H141 2DP sing 31 n n C14 H142 2DP sing 32 n n C14 H143 2DP sing 33 n n C15 C16 2DP sing 34 n n C15 H151 2DP sing 35 n n C15 H152 2DP sing 36 n n C16 C17 2DP sing 37 n n C16 H161 2DP sing 38 n n C16 H162 2DP sing 39 n n C17 C18 2DP sing 40 n n C17 H171 2DP sing 41 n n C17 H172 2DP sing 42 n n C18 C19 2DP sing 43 n n C18 C20 2DP sing 44 n n C18 H18 2DP sing 45 n n C19 H191 2DP sing 46 n n C19 H192 2DP sing 47 n n C19 H193 2DP sing 48 n n C20 C21 2DP sing 49 n n C20 H201 2DP sing 50 n n C20 H202 2DP sing 51 n n C21 C22 2DP sing 52 n n C21 H211 2DP sing 53 n n C21 H212 2DP sing 54 n n C22 C23 2DP sing 55 n n C22 H221 2DP sing 56 n n C22 H222 2DP sing 57 n n C23 C24 2DP sing 58 n n C23 C25 2DP sing 59 n n C23 H23 2DP sing 60 n n C24 H241 2DP sing 61 n n C24 H242 2DP sing 62 n n C24 H243 2DP sing 63 n n C25 C26 2DP sing 64 n n C25 H251 2DP sing 65 n n C25 H252 2DP sing 66 n n C26 C27 2DP sing 67 n n C26 H261 2DP sing 68 n n C26 H262 2DP sing 69 n n C27 C28 2DP sing 70 n n C27 H271 2DP sing 71 n n C27 H272 2DP sing 72 n n C28 C29 2DP sing 73 n n C28 C30 2DP sing 74 n n C28 H28 2DP sing 75 n n C29 H291 2DP sing 76 n n C29 H292 2DP sing 77 n n C29 H293 2DP sing 78 n n C30 H301 2DP sing 79 n n C30 H302 2DP sing 80 n n C30 H303 2DP sing 81 n n C41 C42 2DP sing 82 n n C41 O2 2DP sing 83 n n C41 H411 2DP sing 84 n n C41 H412 2DP sing 85 n n C42 C43 2DP sing 86 n n C42 H421 2DP sing 87 n n C42 H422 2DP sing 88 n n C43 C44 2DP sing 89 n n C43 C45 2DP sing 90 n n C43 H43 2DP sing 91 n n C44 H441 2DP sing 92 n n C44 H442 2DP sing 93 n n C44 H443 2DP sing 94 n n C45 C46 2DP sing 95 n n C45 H451 2DP sing 96 n n C45 H452 2DP sing 97 n n C46 C47 2DP sing 98 n n C46 H461 2DP sing 99 n n C46 H462 2DP sing 100 n n C47 C48 2DP sing 101 n n C47 H471 2DP sing 102 n n C47 H472 2DP sing 103 n n C48 C49 2DP sing 104 n n C48 C50 2DP sing 105 n n C48 H48 2DP sing 106 n n C49 H491 2DP sing 107 n n C49 H492 2DP sing 108 n n C49 H493 2DP sing 109 n n C50 C51 2DP sing 110 n n C50 H501 2DP sing 111 n n C50 H502 2DP sing 112 n n C51 C52 2DP sing 113 n n C51 H511 2DP sing 114 n n C51 H512 2DP sing 115 n n C52 C53 2DP sing 116 n n C52 H521 2DP sing 117 n n C52 H522 2DP sing 118 n n C53 C54 2DP sing 119 n n C53 C55 2DP sing 120 n n C53 H53 2DP sing 121 n n C54 H541 2DP sing 122 n n C54 H542 2DP sing 123 n n C54 H543 2DP sing 124 n n C55 C56 2DP sing 125 n n C55 H551 2DP sing 126 n n C55 H552 2DP sing 127 n n C56 C57 2DP sing 128 n n C56 H561 2DP sing 129 n n C56 H562 2DP sing 130 n n C57 C58 2DP sing 131 n n C57 H571 2DP sing 132 n n C57 H572 2DP sing 133 n n C58 C59 2DP sing 134 n n C58 C60 2DP sing 135 n n C58 H58 2DP sing 136 n n C59 H591 2DP sing 137 n n C59 H592 2DP sing 138 n n C59 H593 2DP sing 139 n n C60 H601 2DP sing 140 n n C60 H602 2DP sing 141 n n C60 H603 2DP sing 142 n n O3 P1 2DP sing 143 n n O4 P1 2DP doub 144 n n O5 P1 2DP sing 145 n n O5 HO5 2DP sing 146 n n O6 P1 2DP sing 147 n n O7 HO7 2DP sing 148 n n O8 P2 2DP sing 149 n n O9 P2 2DP doub 150 n n O10 P2 2DP sing 151 n n O10 HOA 2DP sing 152 n n O11 P2 2DP sing 153 n n O11 CM 2DP sing 154 n n CM HM1 2DP sing 155 n n CM HM2 2DP sing 156 n n CM HM3 2DP sing 157 n n # _atom_sites.entry_id 2AT9 _atom_sites.fract_transf_matrix[1][1] 0.016013 _atom_sites.fract_transf_matrix[1][2] 0.009245 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01849 _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] 0.01 _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 RET A 1 249 216 RET RET A C 3 2DP A 1 261 261 2DP 2DP . D 3 2DP A 1 262 262 2DP 2DP . E 3 2DP A 1 263 263 2DP 2DP . F 3 2DP A 1 264 264 2DP 2DP . G 3 2DP A 1 265 265 2DP 2DP . H 3 2DP A 1 267 267 2DP 2DP . I 3 2DP A 1 268 268 2DP 2DP . J 3 2DP A 1 269 269 2DP 2DP . K 4 HOH A 1 270 1 HOH HOH . K 4 HOH A 2 271 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 C C1 2DP . . . J 3 11.6 -15.801 18.013 1 17.79 ? C1 2DP 269 A 1 HETATM 2 C C2 2DP . . . J 3 11.145 -17.273 18.036 1 17.78 ? C2 2DP 269 A 1 HETATM 3 C C3 2DP . . . J 3 10.466 -17.737 19.369 1 22.58 ? C3 2DP 269 A 1 HETATM 4 C C4 2DP . . . J 3 10.615 -17.495 24.437 1 31.84 ? C4 2DP 269 A 1 HETATM 5 C C5 2DP . . . J 3 10.025 -16.155 25.127 1 31.54 ? C5 2DP 269 A 1 HETATM 6 C C6 2DP . . . J 3 8.685 -15.722 24.402 1 33.92 ? C6 2DP 269 A 1 HETATM 7 C C11 2DP . . . J 3 11.262 -13.64 16.865 1 13.16 ? C11 2DP 269 A 1 HETATM 8 C C12 2DP . . . J 3 11.98 -13.567 15.475 1 11.49 ? C12 2DP 269 A 1 HETATM 9 C C13 2DP . . . J 3 13.127 -12.497 15.351 1 8.82 ? C13 2DP 269 A 1 HETATM 10 C C14 2DP . . . J 3 14.413 -13.156 15.851 1 10.48 ? C14 2DP 269 A 1 HETATM 11 C C15 2DP . . . J 3 13.429 -12.026 13.899 1 5.37 ? C15 2DP 269 A 1 HETATM 12 C C16 2DP . . . J 3 12.275 -12.052 12.881 1 2.73 ? C16 2DP 269 A 1 HETATM 13 C C17 2DP . . . J 3 12.679 -12.399 11.43 1 2 ? C17 2DP 269 A 1 HETATM 14 C C18 2DP . . . J 3 11.841 -11.968 10.184 1 2 ? C18 2DP 269 A 1 HETATM 15 C C19 2DP . . . J 3 11.138 -10.621 10.142 1 2 ? C19 2DP 269 A 1 HETATM 16 C C20 2DP . . . J 3 11.736 -12.883 8.954 1 4.37 ? C20 2DP 269 A 1 HETATM 17 C C21 2DP . . . J 3 12.584 -12.585 7.719 1 4.8 ? C21 2DP 269 A 1 HETATM 18 C C22 2DP . . . J 3 11.911 -12.798 6.365 1 5.36 ? C22 2DP 269 A 1 HETATM 19 C C23 2DP . . . J 3 12.489 -13.85 5.383 1 7.19 ? C23 2DP 269 A 1 HETATM 20 C C24 2DP . . . J 3 11.893 -15.263 5.383 1 8.14 ? C24 2DP 269 A 1 HETATM 21 C C25 2DP . . . J 3 13.648 -13.487 4.398 1 7.47 ? C25 2DP 269 A 1 HETATM 22 C C26 2DP . . . J 3 14.853 -14.458 4.353 1 9.56 ? C26 2DP 269 A 1 HETATM 23 C C27 2DP . . . J 3 15.934 -13.772 3.547 1 12.06 ? C27 2DP 269 A 1 HETATM 24 C C28 2DP . . . J 3 17.141 -14.565 3.081 1 10.91 ? C28 2DP 269 A 1 HETATM 25 C C29 2DP . . . J 3 17.451 -14.314 1.629 1 9.47 ? C29 2DP 269 A 1 HETATM 26 C C30 2DP . . . J 3 17.038 -16.078 3.328 1 10.03 ? C30 2DP 269 A 1 HETATM 27 C C41 2DP . . . J 3 12.474 -18.638 16.352 1 19.91 ? C41 2DP 269 A 1 HETATM 28 C C42 2DP . . . J 3 13.993 -19.06 16.254 1 22.2 ? C42 2DP 269 A 1 HETATM 29 C C43 2DP . . . J 3 14.645 -19.703 14.923 1 23.46 ? C43 2DP 269 A 1 HETATM 30 C C44 2DP . . . J 3 14.161 -18.946 13.605 1 24.29 ? C44 2DP 269 A 1 HETATM 31 C C45 2DP . . . J 3 16.274 -19.77 15.038 1 23.75 ? C45 2DP 269 A 1 HETATM 32 C C46 2DP . . . J 3 17.297 -18.997 14.085 1 23.49 ? C46 2DP 269 A 1 HETATM 33 C C47 2DP . . . J 3 18.004 -19.746 12.877 1 22.67 ? C47 2DP 269 A 1 HETATM 34 C C48 2DP . . . J 3 17.301 -19.875 11.447 1 23.32 ? C48 2DP 269 A 1 HETATM 35 C C49 2DP . . . J 3 16.096 -20.85 11.483 1 21.72 ? C49 2DP 269 A 1 HETATM 36 C C50 2DP . . . J 3 18.318 -20.357 10.376 1 22.44 ? C50 2DP 269 A 1 HETATM 37 C C51 2DP . . . J 3 17.811 -20.234 8.907 1 22.17 ? C51 2DP 269 A 1 HETATM 38 C C52 2DP . . . J 3 18.118 -21.414 7.979 1 19.28 ? C52 2DP 269 A 1 HETATM 39 C C53 2DP . . . J 3 19.635 -21.728 7.709 1 19.87 ? C53 2DP 269 A 1 HETATM 40 C C54 2DP . . . J 3 20.054 -23.208 7.991 1 18.81 ? C54 2DP 269 A 1 HETATM 41 C C55 2DP . . . J 3 19.961 -21.2 6.231 1 19.31 ? C55 2DP 269 A 1 HETATM 42 C C56 2DP . . . J 3 20.042 -22.18 5.044 1 18.56 ? C56 2DP 269 A 1 HETATM 43 C C57 2DP . . . J 3 19.365 -21.704 3.74 1 17.64 ? C57 2DP 269 A 1 HETATM 44 C C58 2DP . . . J 3 17.903 -22.18 3.535 1 18.42 ? C58 2DP 269 A 1 HETATM 45 C C59 2DP . . . J 3 16.848 -21.288 4.229 1 19.2 ? C59 2DP 269 A 1 HETATM 46 C C60 2DP . . . J 3 17.548 -22.342 2.039 1 18 ? C60 2DP 269 A 1 HETATM 47 O O1 2DP . . . J 3 10.764 -15.003 17.107 1 15.85 ? O1 2DP 269 A 1 HETATM 48 O O2 2DP . . . J 3 12.274 -18.139 17.729 1 18.91 ? O2 2DP 269 A 1 HETATM 49 O O3 2DP . . . J 3 10.605 -16.753 20.469 1 27.33 ? O3 2DP 269 A 1 HETATM 50 O O4 2DP . . . J 3 12.246 -15.649 22.221 1 30.18 ? O4 2DP 269 A 1 HETATM 51 O O5 2DP . . . J 3 12.72 -18.008 21.398 1 29.98 ? O5 2DP 269 A 1 HETATM 52 O O6 2DP . . . J 3 10.572 -17.603 22.923 1 31.36 ? O6 2DP 269 A 1 HETATM 53 O O7 2DP . . . J 3 10.933 -15.008 25.034 1 32.27 ? O7 2DP 269 A 1 HETATM 54 O O8 2DP . . . J 3 7.603 -15.225 25.299 1 35.2 ? O8 2DP 269 A 1 HETATM 55 O O9 2DP . . . J 3 5.28 -16.379 24.778 1 35.22 ? O9 2DP 269 A 1 HETATM 56 O O10 2DP . . . J 3 5.285 -13.975 25.623 1 34.05 ? O10 2DP 269 A 1 HETATM 57 O O11 2DP . . . J 3 6.033 -14.489 23.288 1 35.41 ? O11 2DP 269 A 1 HETATM 58 P P1 2DP . . . J 3 11.655 -16.976 21.775 1 30.22 ? P1 2DP 269 A 1 HETATM 59 P P2 2DP . . . J 3 6.01 -15.013 24.724 1 35.91 ? P2 2DP 269 A 1 HETATM 60 C CM 2DP . . . J 3 6.222 -15.316 22.053 1 36.5 ? CM 2DP 269 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 60 #