data_2AT9 # _model_server_result.job_id M08_5nWcdXWj8YnsfnSyxA _model_server_result.datetime_utc '2024-12-26 15:07:35' _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":"C","auth_seq_id":261}' # _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 . . . C 3 2.349 5.989 -12.643 1 15.53 ? C1 2DP 261 A 1 HETATM 2 C C2 2DP . . . C 3 1.578 5.408 -13.846 1 17.54 ? C2 2DP 261 A 1 HETATM 3 C C3 2DP . . . C 3 1.256 6.46 -14.947 1 19.15 ? C3 2DP 261 A 1 HETATM 4 C C4 2DP . . . C 3 2.681 4.585 -19.101 1 21.87 ? C4 2DP 261 A 1 HETATM 5 C C5 2DP . . . C 3 3.843 5.347 -19.927 1 19.9 ? C5 2DP 261 A 1 HETATM 6 C C6 2DP . . . C 3 3.204 6.074 -21.165 1 19.29 ? C6 2DP 261 A 1 HETATM 7 C C11 2DP . . . C 3 2.3 5.02 -10.4 1 13.98 ? C11 2DP 261 A 1 HETATM 8 C C12 2DP . . . C 3 1.659 5.285 -9.007 1 14.11 ? C12 2DP 261 A 1 HETATM 9 C C13 2DP . . . C 3 2.534 6.072 -7.969 1 13.32 ? C13 2DP 261 A 1 HETATM 10 C C14 2DP . . . C 3 2.809 7.448 -8.549 1 13.56 ? C14 2DP 261 A 1 HETATM 11 C C15 2DP . . . C 3 1.822 6.3 -6.599 1 14.38 ? C15 2DP 261 A 1 HETATM 12 C C16 2DP . . . C 3 2.576 5.779 -5.337 1 14.24 ? C16 2DP 261 A 1 HETATM 13 C C17 2DP . . . C 3 2.896 6.809 -4.209 1 9.78 ? C17 2DP 261 A 1 HETATM 14 C C18 2DP . . . C 3 1.773 7.62 -3.456 1 7.81 ? C18 2DP 261 A 1 HETATM 15 C C19 2DP . . . C 3 0.374 7.06 -3.37 1 8.12 ? C19 2DP 261 A 1 HETATM 16 C C20 2DP . . . C 3 2.061 9.008 -2.78 1 6.25 ? C20 2DP 261 A 1 HETATM 17 C C21 2DP . . . C 3 1.633 9.316 -1.322 1 2 ? C21 2DP 261 A 1 HETATM 18 C C22 2DP . . . C 3 1.922 8.227 -0.26 1 2 ? C22 2DP 261 A 1 HETATM 19 C C23 2DP . . . C 3 1.906 8.562 1.246 1 2 ? C23 2DP 261 A 1 HETATM 20 C C24 2DP . . . C 3 2.171 9.99 1.659 1 2 ? C24 2DP 261 A 1 HETATM 21 C C25 2DP . . . C 3 1.627 7.472 2.331 1 4.06 ? C25 2DP 261 A 1 HETATM 22 C C26 2DP . . . C 3 2.374 7.626 3.687 1 7.48 ? C26 2DP 261 A 1 HETATM 23 C C27 2DP . . . C 3 1.423 8.256 4.681 1 13.99 ? C27 2DP 261 A 1 HETATM 24 C C28 2DP . . . C 3 1.507 7.752 6.104 1 18.73 ? C28 2DP 261 A 1 HETATM 25 C C29 2DP . . . C 3 1.009 6.315 6.3 1 17.74 ? C29 2DP 261 A 1 HETATM 26 C C30 2DP . . . C 3 0.785 8.691 7.071 1 19.68 ? C30 2DP 261 A 1 HETATM 27 C C41 2DP . . . C 3 -0.887 5.435 -13.022 1 14.49 ? C41 2DP 261 A 1 HETATM 28 C C42 2DP . . . C 3 -1.826 4.343 -12.383 1 11.39 ? C42 2DP 261 A 1 HETATM 29 C C43 2DP . . . C 3 -3.412 4.492 -12.359 1 8.02 ? C43 2DP 261 A 1 HETATM 30 C C44 2DP . . . C 3 -4.034 4.344 -13.793 1 8.49 ? C44 2DP 261 A 1 HETATM 31 C C45 2DP . . . C 3 -4.076 3.444 -11.367 1 6.16 ? C45 2DP 261 A 1 HETATM 32 C C46 2DP . . . C 3 -4.557 3.871 -9.936 1 7.61 ? C46 2DP 261 A 1 HETATM 33 C C47 2DP . . . C 3 -3.505 4.413 -8.884 1 7.15 ? C47 2DP 261 A 1 HETATM 34 C C48 2DP . . . C 3 -2.932 3.535 -7.699 1 7.27 ? C48 2DP 261 A 1 HETATM 35 C C49 2DP . . . C 3 -2.921 2.024 -8.018 1 8.52 ? C49 2DP 261 A 1 HETATM 36 C C50 2DP . . . C 3 -3.754 3.801 -6.43 1 9.95 ? C50 2DP 261 A 1 HETATM 37 C C51 2DP . . . C 3 -2.942 4.361 -5.249 1 13.55 ? C51 2DP 261 A 1 HETATM 38 C C52 2DP . . . C 3 -2.091 3.331 -4.492 1 17.42 ? C52 2DP 261 A 1 HETATM 39 C C53 2DP . . . C 3 -1.016 3.862 -3.459 1 18.83 ? C53 2DP 261 A 1 HETATM 40 C C54 2DP . . . C 3 -1.384 3.608 -1.954 1 19.99 ? C54 2DP 261 A 1 HETATM 41 C C55 2DP . . . C 3 0.399 3.258 -3.915 1 21.38 ? C55 2DP 261 A 1 HETATM 42 C C56 2DP . . . C 3 1.203 2.35 -2.955 1 23.09 ? C56 2DP 261 A 1 HETATM 43 C C57 2DP . . . C 3 2.468 2.971 -2.311 1 24.28 ? C57 2DP 261 A 1 HETATM 44 C C58 2DP . . . C 3 2.245 4.171 -1.34 1 26.55 ? C58 2DP 261 A 1 HETATM 45 C C59 2DP . . . C 3 1.605 3.802 0.034 1 25.78 ? C59 2DP 261 A 1 HETATM 46 C C60 2DP . . . C 3 3.563 4.973 -1.124 1 28.36 ? C60 2DP 261 A 1 HETATM 47 O O1 2DP . . . C 3 1.613 5.824 -11.398 1 13.98 ? O1 2DP 261 A 1 HETATM 48 O O2 2DP . . . C 3 0.36 4.723 -13.384 1 15.75 ? O2 2DP 261 A 1 HETATM 49 O O3 2DP . . . C 3 1.784 6.025 -16.267 1 22.31 ? O3 2DP 261 A 1 HETATM 50 O O4 2DP . . . C 3 2.091 7.838 -18.176 1 23.96 ? O4 2DP 261 A 1 HETATM 51 O O5 2DP . . . C 3 -0.244 7.056 -17.608 1 23.52 ? O5 2DP 261 A 1 HETATM 52 O O6 2DP . . . C 3 1.414 5.337 -18.772 1 22.87 ? O6 2DP 261 A 1 HETATM 53 O O7 2DP . . . C 3 4.891 4.456 -20.45 1 19.55 ? O7 2DP 261 A 1 HETATM 54 O O8 2DP . . . C 3 4.15 6.295 -22.263 1 20.64 ? O8 2DP 261 A 1 HETATM 55 O O9 2DP . . . C 3 2.678 4.642 -23.706 1 20.19 ? O9 2DP 261 A 1 HETATM 56 O O10 2DP . . . C 3 3.668 6.764 -24.791 1 20.95 ? O10 2DP 261 A 1 HETATM 57 O O11 2DP . . . C 3 5.122 4.814 -24.176 1 20.81 ? O11 2DP 261 A 1 HETATM 58 P P1 2DP . . . C 3 1.224 6.672 -17.745 1 24.8 ? P1 2DP 261 A 1 HETATM 59 P P2 2DP . . . C 3 3.894 5.605 -23.776 1 21.87 ? P2 2DP 261 A 1 HETATM 60 C CM 2DP . . . C 3 5.16 3.84 -25.318 1 22.16 ? CM 2DP 261 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 60 #