data_5EBM # _model_server_result.job_id frTiRcYuedg5cDYoGxZZbw _model_server_result.datetime_utc '2025-03-04 23:32:03' _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 5ebm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 5EBM # _exptl.entry_id 5EBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 625.018 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIACYL GLYCEROL' _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 5EBM _cell.length_a 155.72 _cell.length_b 155.72 _cell.length_c 75.556 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K 1 1 A,B,C,D,E,F,G,H,I,J,K 1 2 A,B,C,D,E,F,G,H,I,J,K 1 3 A,B,C,D,E,F,G,H,I,J,K 1 4 # 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_595 -x,-y+4,z -1 0 0 0 -1 0 0 0 1 0 622.88 0 3 'crystal symmetry operation' 3_775 -y+2,x+2,z 0 -1 0 1 0 0 0 0 1 311.44 311.44 0 4 'crystal symmetry operation' 4_375 y-2,-x+2,z 0 1 0 -1 0 0 0 0 1 -311.44 311.44 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 22 A CYS 22 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 145 A CYS 145 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 B SG CYS 23 B CYS 23 1_555 B SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 B SG CYS 134 B CYS 134 1_555 B SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc1 C O GLY 75 C GLY 75 1_555 G K K . C K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc2 C O GLY 75 C GLY 75 1_555 G K K . C K 1004 3_775 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc3 C O GLY 77 C GLY 77 1_555 F K K . C K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc4 C O GLY 77 C GLY 77 1_555 F K K . C K 1003 4_375 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? # _chem_comp.formula 'C39 H76 O5' _chem_comp.formula_weight 625.018 _chem_comp.id DGA _chem_comp.mon_nstd_flag . _chem_comp.name 'DIACYL 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 CA1 CA2 DGA sing 83 n n CA1 OA1 DGA doub 84 n n CA1 OG1 DGA sing 85 n n CA2 CA3 DGA sing 86 n n CA2 HA21 DGA sing 87 n n CA2 HA22 DGA sing 88 n n CA3 CA4 DGA sing 89 n n CA3 HA31 DGA sing 90 n n CA3 HA32 DGA sing 91 n n CA4 CA5 DGA sing 92 n n CA4 HA41 DGA sing 93 n n CA4 HA42 DGA sing 94 n n CA5 CA6 DGA sing 95 n n CA5 HA51 DGA sing 96 n n CA5 HA52 DGA sing 97 n n CA6 CA7 DGA sing 98 n n CA6 HA61 DGA sing 99 n n CA6 HA62 DGA sing 100 n n CA7 CA8 DGA sing 101 n n CA7 HA71 DGA sing 102 n n CA7 HA72 DGA sing 103 n n CA8 CA9 DGA sing 104 n n CA8 HA81 DGA sing 105 n n CA8 HA82 DGA sing 106 n n CA9 CAA DGA sing 107 n n CA9 HA91 DGA sing 108 n n CA9 HA92 DGA sing 109 n n CAA CBA DGA sing 110 n n CAA HAT1 DGA sing 111 n n CAA HAT2 DGA sing 112 n n CBA CCA DGA sing 113 n n CBA HAE1 DGA sing 114 n n CBA HAE2 DGA sing 115 n n CCA CDA DGA sing 116 n n CCA HAW1 DGA sing 117 n n CCA HAW2 DGA sing 118 n n CDA CEA DGA sing 119 n n CDA HAH1 DGA sing 120 n n CDA HAH2 DGA sing 121 n n CEA CFA DGA sing 122 n n CEA HAF1 DGA sing 123 n n CEA HAF2 DGA sing 124 n n CFA CGA DGA sing 125 n n CFA HAN1 DGA sing 126 n n CFA HAN2 DGA sing 127 n n CGA CHA DGA sing 128 n n CGA HAS1 DGA sing 129 n n CGA HAS2 DGA sing 130 n n CHA CIA DGA sing 131 n n CHA HAV1 DGA sing 132 n n CHA HAV2 DGA sing 133 n n CIA HAG1 DGA sing 134 n n CIA HAG2 DGA sing 135 n n CIA HAG3 DGA sing 136 n n CB1 CB2 DGA sing 137 n n CB1 OB1 DGA doub 138 n n CB1 OG2 DGA sing 139 n n CB2 CB3 DGA sing 140 n n CB2 HB21 DGA sing 141 n n CB2 HB22 DGA sing 142 n n CB3 CB4 DGA sing 143 n n CB3 HB31 DGA sing 144 n n CB3 HB32 DGA sing 145 n n CB4 CB5 DGA sing 146 n n CB4 HB41 DGA sing 147 n n CB4 HB42 DGA sing 148 n n CB5 CB6 DGA sing 149 n n CB5 HB51 DGA sing 150 n n CB5 HB52 DGA sing 151 n n CB6 CB7 DGA sing 152 n n CB6 HB61 DGA sing 153 n n CB6 HB62 DGA sing 154 n n CB7 CB8 DGA sing 155 n n CB7 HB71 DGA sing 156 n n CB7 HB72 DGA sing 157 n n CB8 CB9 DGA sing 158 n n CB8 HB81 DGA sing 159 n n CB8 HB82 DGA sing 160 n n CB9 CAB DGA sing 161 n n CB9 HB91 DGA sing 162 n n CB9 HB92 DGA sing 163 n n CAB CBB DGA sing 164 n n CAB HBT1 DGA sing 165 n n CAB HBT2 DGA sing 166 n n CBB CCB DGA sing 167 n n CBB HBE1 DGA sing 168 n n CBB HBE2 DGA sing 169 n n CCB CDB DGA sing 170 n n CCB HBW1 DGA sing 171 n n CCB HBW2 DGA sing 172 n n CDB CEB DGA sing 173 n n CDB HBH1 DGA sing 174 n n CDB HBH2 DGA sing 175 n n CEB CFB DGA sing 176 n n CEB HBF1 DGA sing 177 n n CEB HBF2 DGA sing 178 n n CFB CGB DGA sing 179 n n CFB HBN1 DGA sing 180 n n CFB HBN2 DGA sing 181 n n CGB CHB DGA sing 182 n n CGB HBS1 DGA sing 183 n n CGB HBS2 DGA sing 184 n n CHB CIB DGA sing 185 n n CHB HBV1 DGA sing 186 n n CHB HBV2 DGA sing 187 n n CIB HBG1 DGA sing 188 n n CIB HBG2 DGA sing 189 n n CIB HBG3 DGA sing 190 n n OG1 CG1 DGA sing 191 n n CG1 CG2 DGA sing 192 n n CG1 HG11 DGA sing 193 n n CG1 HG12 DGA sing 194 n n CG2 OG2 DGA sing 195 n n CG2 CG3 DGA sing 196 n n CG2 HG2 DGA sing 197 n n CG3 OXT DGA sing 198 n n CG3 HG31 DGA sing 199 n n CG3 HG32 DGA sing 200 n n OXT HXT DGA sing 201 n n # _atom_sites.entry_id 5EBM _atom_sites.fract_transf_matrix[1][1] 0.006422 _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] 0.006422 _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] 0.013235 _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 D 4 DGA C 1 1001 1001 DGA DGA . E 5 F09 C 1 1002 1002 F09 F09 . F 6 K C 1 1003 1 K K . G 6 K C 1 1004 2 K K . H 6 K C 1 1005 3 K K . I 7 HOH A 1 301 120 HOH HOH . I 7 HOH A 2 302 96 HOH HOH . I 7 HOH A 3 303 44 HOH HOH . I 7 HOH A 4 304 90 HOH HOH . I 7 HOH A 5 305 29 HOH HOH . I 7 HOH A 6 306 73 HOH HOH . I 7 HOH A 7 307 68 HOH HOH . I 7 HOH A 8 308 20 HOH HOH . I 7 HOH A 9 309 78 HOH HOH . I 7 HOH A 10 310 67 HOH HOH . I 7 HOH A 11 311 86 HOH HOH . I 7 HOH A 12 312 83 HOH HOH . I 7 HOH A 13 313 35 HOH HOH . I 7 HOH A 14 314 31 HOH HOH . I 7 HOH A 15 315 76 HOH HOH . I 7 HOH A 16 316 82 HOH HOH . I 7 HOH A 17 317 92 HOH HOH . I 7 HOH A 18 318 95 HOH HOH . I 7 HOH A 19 319 58 HOH HOH . I 7 HOH A 20 320 126 HOH HOH . I 7 HOH A 21 321 116 HOH HOH . I 7 HOH A 22 322 50 HOH HOH . I 7 HOH A 23 323 4 HOH HOH . I 7 HOH A 24 324 63 HOH HOH . I 7 HOH A 25 325 11 HOH HOH . I 7 HOH A 26 326 15 HOH HOH . I 7 HOH A 27 327 113 HOH HOH . I 7 HOH A 28 328 37 HOH HOH . I 7 HOH A 29 329 38 HOH HOH . I 7 HOH A 30 330 87 HOH HOH . I 7 HOH A 31 331 127 HOH HOH . I 7 HOH A 32 332 69 HOH HOH . I 7 HOH A 33 333 39 HOH HOH . I 7 HOH A 34 334 85 HOH HOH . J 7 HOH B 1 301 71 HOH HOH . J 7 HOH B 2 302 64 HOH HOH . J 7 HOH B 3 303 124 HOH HOH . J 7 HOH B 4 304 18 HOH HOH . J 7 HOH B 5 305 36 HOH HOH . J 7 HOH B 6 306 13 HOH HOH . J 7 HOH B 7 307 19 HOH HOH . J 7 HOH B 8 308 27 HOH HOH . J 7 HOH B 9 309 3 HOH HOH . J 7 HOH B 10 310 12 HOH HOH . J 7 HOH B 11 311 80 HOH HOH . J 7 HOH B 12 312 100 HOH HOH . J 7 HOH B 13 313 5 HOH HOH . J 7 HOH B 14 314 23 HOH HOH . J 7 HOH B 15 315 21 HOH HOH . J 7 HOH B 16 316 16 HOH HOH . J 7 HOH B 17 317 42 HOH HOH . J 7 HOH B 18 318 10 HOH HOH . J 7 HOH B 19 319 22 HOH HOH . J 7 HOH B 20 320 65 HOH HOH . J 7 HOH B 21 321 123 HOH HOH . J 7 HOH B 22 322 46 HOH HOH . J 7 HOH B 23 323 25 HOH HOH . J 7 HOH B 24 324 97 HOH HOH . J 7 HOH B 25 325 111 HOH HOH . J 7 HOH B 26 326 121 HOH HOH . J 7 HOH B 27 327 103 HOH HOH . J 7 HOH B 28 328 105 HOH HOH . J 7 HOH B 29 329 17 HOH HOH . J 7 HOH B 30 330 49 HOH HOH . J 7 HOH B 31 331 57 HOH HOH . J 7 HOH B 32 332 43 HOH HOH . J 7 HOH B 33 333 91 HOH HOH . J 7 HOH B 34 334 104 HOH HOH . K 7 HOH C 1 1101 128 HOH HOH . K 7 HOH C 2 1102 129 HOH HOH . K 7 HOH C 3 1103 8 HOH HOH . K 7 HOH C 4 1104 53 HOH HOH . K 7 HOH C 5 1105 130 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 CA1 DGA . . . D 4 -9.568 294.681 28.484 1 85.11 ? CA1 DGA 1001 C 1 HETATM 2 C CA2 DGA . . . D 4 -10.387 294.94 29.725 1 83.87 ? CA2 DGA 1001 C 1 HETATM 3 C CA3 DGA . . . D 4 -9.69 295.987 30.585 1 82.2 ? CA3 DGA 1001 C 1 HETATM 4 C CA4 DGA . . . D 4 -10.33 296.076 31.965 1 80.91 ? CA4 DGA 1001 C 1 HETATM 5 C CA5 DGA . . . D 4 -9.346 295.659 33.052 1 79.9 ? CA5 DGA 1001 C 1 HETATM 6 C CA6 DGA . . . D 4 -9.331 296.671 34.191 1 79.21 ? CA6 DGA 1001 C 1 HETATM 7 C CA7 DGA . . . D 4 -9.271 295.969 35.543 1 78.74 ? CA7 DGA 1001 C 1 HETATM 8 C CA8 DGA . . . D 4 -9.987 296.784 36.614 1 78.6 ? CA8 DGA 1001 C 1 HETATM 9 C CA9 DGA . . . D 4 -9.801 296.16 37.991 1 78.83 ? CA9 DGA 1001 C 1 HETATM 10 O OA1 DGA . . . D 4 -8.876 295.562 28 1 84.78 ? OA1 DGA 1001 C 1 HETATM 11 C CB1 DGA . . . D 4 -12.729 291.943 28.686 1 90.8 ? CB1 DGA 1001 C 1 HETATM 12 C CB2 DGA . . . D 4 -12.508 292.173 30.162 1 90.73 ? CB2 DGA 1001 C 1 HETATM 13 C CB3 DGA . . . D 4 -13.855 292.253 30.871 1 90.43 ? CB3 DGA 1001 C 1 HETATM 14 C CB4 DGA . . . D 4 -14.027 293.597 31.568 1 89.93 ? CB4 DGA 1001 C 1 HETATM 15 C CB5 DGA . . . D 4 -15.107 293.522 32.641 1 89.67 ? CB5 DGA 1001 C 1 HETATM 16 C CB6 DGA . . . D 4 -16.414 294.128 32.143 1 89.49 ? CB6 DGA 1001 C 1 HETATM 17 C CB7 DGA . . . D 4 -17.016 295.06 33.188 1 89.16 ? CB7 DGA 1001 C 1 HETATM 18 C CB8 DGA . . . D 4 -17.938 296.085 32.539 1 88.61 ? CB8 DGA 1001 C 1 HETATM 19 C CB9 DGA . . . D 4 -17.739 297.466 33.153 1 88.47 ? CB9 DGA 1001 C 1 HETATM 20 C CAB DGA . . . D 4 -18.994 298.317 33.004 1 88.34 ? CAB DGA 1001 C 1 HETATM 21 C CBB DGA . . . D 4 -20.207 297.609 33.596 1 87.9 ? CBB DGA 1001 C 1 HETATM 22 C CCB DGA . . . D 4 -21.464 298.457 33.441 1 87.55 ? CCB DGA 1001 C 1 HETATM 23 C CDB DGA . . . D 4 -21.689 299.329 34.67 1 87.56 ? CDB DGA 1001 C 1 HETATM 24 C CEB DGA . . . D 4 -21.987 300.769 34.271 1 87.6 ? CEB DGA 1001 C 1 HETATM 25 O OB1 DGA . . . D 4 -13.265 290.921 28.289 1 90.98 ? OB1 DGA 1001 C 1 HETATM 26 O OG1 DGA . . . D 4 -9.596 293.373 27.849 1 86.53 ? OG1 DGA 1001 C 1 HETATM 27 C CG1 DGA . . . D 4 -10.204 293.215 26.569 1 88.71 ? CG1 DGA 1001 C 1 HETATM 28 C CG2 DGA . . . D 4 -11.47 292.378 26.708 1 90.38 ? CG2 DGA 1001 C 1 HETATM 29 O OG2 DGA . . . D 4 -12.304 292.941 27.719 1 90.79 ? OG2 DGA 1001 C 1 HETATM 30 C CG3 DGA . . . D 4 -12.219 292.364 25.381 1 91.61 ? CG3 DGA 1001 C 1 HETATM 31 O OXT DGA . . . D 4 -11.764 291.263 24.588 1 93.61 ? OXT DGA 1001 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #