data_4PD4 # _model_server_result.job_id AMvCuj2kYZPjCetrgBbzPw _model_server_result.datetime_utc '2024-11-16 21:42:45' _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 4pd4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":502}' # _entry.id 4PD4 # _exptl.entry_id 4PD4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 704.998 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.18 _cell.angle_gamma 90 _cell.entry_id 4PD4 _cell.length_a 212.26 _cell.length_b 150.88 _cell.length_c 143.09 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PD4 _symmetry.cell_setting . _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 22-meric _pdbx_struct_assembly.oligomeric_count 22 _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,L,M,N,O,P,Q,R,S,T,U,V _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_756 -x+2,y,-z+1 -1 0 0 0 1 0 0 0 -1 363.640439 0 129.492962 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 13 M N N ? 13 S N N ? 13 V 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 134 E CYS 164 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf2 F SG CYS 28 F CYS 101 1_555 F SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 K SG CYS 23 K CYS 23 1_555 K SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc1 C NE2 HIS 82 C HIS 82 1_555 N FE HEM . C HEM 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc2 C NE2 HIS 96 C HIS 96 1_555 O FE HEM . C HEM 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 N FE HEM . C HEM 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 O FE HEM . C HEM 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 T FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 D SD MET 164 D MET 225 1_555 T FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc7 E SG CYS 129 E CYS 159 1_555 U FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc8 E ND1 HIS 131 E HIS 161 1_555 U FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc9 E SG CYS 148 E CYS 178 1_555 U FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc10 E ND1 HIS 151 E HIS 181 1_555 U FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? # _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 133 n n O13 H13 3PH sing 134 n n P O14 3PH sing 135 n n P O12 3PH doub 136 n n P O11 3PH sing 137 n n O11 C1 3PH sing 138 n n C1 C2 3PH sing 139 n n C1 H11 3PH sing 140 n n C1 H12 3PH sing 141 n n C2 O21 3PH sing 142 n n C2 C3 3PH sing 143 n n C2 H2 3PH sing 144 n n O21 C21 3PH sing 145 n n C21 O22 3PH doub 146 n n C21 C22 3PH sing 147 n n C22 C23 3PH sing 148 n n C22 H221 3PH sing 149 n n C22 H222 3PH sing 150 n n C23 C24 3PH sing 151 n n C23 H231 3PH sing 152 n n C23 H232 3PH sing 153 n n C24 C25 3PH sing 154 n n C24 H241 3PH sing 155 n n C24 H242 3PH sing 156 n n C25 C26 3PH sing 157 n n C25 H251 3PH sing 158 n n C25 H252 3PH sing 159 n n C26 C27 3PH sing 160 n n C26 H261 3PH sing 161 n n C26 H262 3PH sing 162 n n C27 C28 3PH sing 163 n n C27 H271 3PH sing 164 n n C27 H272 3PH sing 165 n n C28 C29 3PH sing 166 n n C28 H281 3PH sing 167 n n C28 H282 3PH sing 168 n n C29 C2A 3PH sing 169 n n C29 H291 3PH sing 170 n n C29 H292 3PH sing 171 n n C2A C2B 3PH sing 172 n n C2A H2A1 3PH sing 173 n n C2A H2A2 3PH sing 174 n n C2B C2C 3PH sing 175 n n C2B H2B1 3PH sing 176 n n C2B H2B2 3PH sing 177 n n C2C C2D 3PH sing 178 n n C2C H2C1 3PH sing 179 n n C2C H2C2 3PH sing 180 n n C2D C2E 3PH sing 181 n n C2D H2D1 3PH sing 182 n n C2D H2D2 3PH sing 183 n n C2E C2F 3PH sing 184 n n C2E H2E1 3PH sing 185 n n C2E H2E2 3PH sing 186 n n C2F C2G 3PH sing 187 n n C2F H2F1 3PH sing 188 n n C2F H2F2 3PH sing 189 n n C2G C2H 3PH sing 190 n n C2G H2G1 3PH sing 191 n n C2G H2G2 3PH sing 192 n n C2H C2I 3PH sing 193 n n C2H H2H1 3PH sing 194 n n C2H H2H2 3PH sing 195 n n C2I H2I1 3PH sing 196 n n C2I H2I2 3PH sing 197 n n C2I H2I3 3PH sing 198 n n C3 O31 3PH sing 199 n n C3 H31 3PH sing 200 n n C3 H32 3PH sing 201 n n O31 C31 3PH sing 202 n n C31 O32 3PH doub 203 n n C31 C32 3PH sing 204 n n C32 C33 3PH sing 205 n n C32 H321 3PH sing 206 n n C32 H322 3PH sing 207 n n C33 C34 3PH sing 208 n n C33 H331 3PH sing 209 n n C33 H332 3PH sing 210 n n C34 C35 3PH sing 211 n n C34 H341 3PH sing 212 n n C34 H342 3PH sing 213 n n C35 C36 3PH sing 214 n n C35 H351 3PH sing 215 n n C35 H352 3PH sing 216 n n C36 C37 3PH sing 217 n n C36 H361 3PH sing 218 n n C36 H362 3PH sing 219 n n C37 C38 3PH sing 220 n n C37 H371 3PH sing 221 n n C37 H372 3PH sing 222 n n C38 C39 3PH sing 223 n n C38 H381 3PH sing 224 n n C38 H382 3PH sing 225 n n C39 C3A 3PH sing 226 n n C39 H391 3PH sing 227 n n C39 H392 3PH sing 228 n n C3A C3B 3PH sing 229 n n C3A H3A1 3PH sing 230 n n C3A H3A2 3PH sing 231 n n C3B C3C 3PH sing 232 n n C3B H3B1 3PH sing 233 n n C3B H3B2 3PH sing 234 n n C3C C3D 3PH sing 235 n n C3C H3C1 3PH sing 236 n n C3C H3C2 3PH sing 237 n n C3D C3E 3PH sing 238 n n C3D H3D1 3PH sing 239 n n C3D H3D2 3PH sing 240 n n C3E C3F 3PH sing 241 n n C3E H3E1 3PH sing 242 n n C3E H3E2 3PH sing 243 n n C3F C3G 3PH sing 244 n n C3F H3F1 3PH sing 245 n n C3F H3F2 3PH sing 246 n n C3G C3H 3PH sing 247 n n C3G H3G1 3PH sing 248 n n C3G H3G2 3PH sing 249 n n C3H C3I 3PH sing 250 n n C3H H3H1 3PH sing 251 n n C3H H3H2 3PH sing 252 n n C3I H3I1 3PH sing 253 n n C3I H3I2 3PH sing 254 n n C3I H3I3 3PH sing 255 n n O14 H77 3PH sing 256 n n # _atom_sites.entry_id 4PD4 _atom_sites.fract_transf_matrix[1][1] 0.004711 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002215 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006628 _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] 0.007722 _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 L 12 UMQ A 1 501 721 UMQ UMQ . M 13 3PH A 1 502 713 3PH 3PH . N 14 HEM C 1 4001 4001 HEM HEM . O 14 HEM C 1 4002 4002 HEM HEM . P 15 AOQ C 1 4003 1 AOQ AOQ . Q 16 3PE C 1 4004 711 3PE 3PE . R 17 UQ6 C 1 4005 506 UQ6 UQ6 . S 13 3PH C 1 4006 710 3PH 3PH . T 14 HEM D 1 401 4003 HEM HEM . U 18 FES E 1 301 4004 FES FES . V 13 3PH E 1 302 714 3PH 3PH . # 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 . . . M 13 197.843 4.43 42.308 1 28.47 ? O13 3PH 502 A 1 HETATM 2 P P 3PH . . . M 13 199.088 4.032 43.122 1 35.31 ? P 3PH 502 A 1 HETATM 3 O O14 3PH . . . M 13 199.279 4.842 44.395 1 20.97 ? O14 3PH 502 A 1 HETATM 4 O O12 3PH . . . M 13 200.351 3.812 42.308 1 24.66 ? O12 3PH 502 A 1 HETATM 5 O O11 3PH . . . M 13 198.808 2.504 43.632 1 38.52 ? O11 3PH 502 A 1 HETATM 6 C C1 3PH . . . M 13 197.653 2.247 44.451 1 33 ? C1 3PH 502 A 1 HETATM 7 C C2 3PH . . . M 13 197.296 0.773 44.594 1 24.45 ? C2 3PH 502 A 1 HETATM 8 O O21 3PH . . . M 13 197.869 0.37 45.83 1 30.22 ? O21 3PH 502 A 1 HETATM 9 C C21 3PH . . . M 13 197.003 -0.329 46.771 1 29.57 ? C21 3PH 502 A 1 HETATM 10 O O22 3PH . . . M 13 196.182 0.286 47.451 1 33.81 ? O22 3PH 502 A 1 HETATM 11 C C22 3PH . . . M 13 197.184 -1.825 46.915 1 17.57 ? C22 3PH 502 A 1 HETATM 12 C C23 3PH . . . M 13 197.111 -2.284 48.366 1 13.35 ? C23 3PH 502 A 1 HETATM 13 C C24 3PH . . . M 13 198.089 -3.445 48.523 1 16.39 ? C24 3PH 502 A 1 HETATM 14 C C25 3PH . . . M 13 197.672 -4.415 49.628 1 20.25 ? C25 3PH 502 A 1 HETATM 15 C C26 3PH . . . M 13 198.547 -4.313 50.874 1 17.32 ? C26 3PH 502 A 1 HETATM 16 C C3 3PH . . . M 13 197.965 -0.042 43.503 1 25.72 ? C3 3PH 502 A 1 HETATM 17 O O31 3PH . . . M 13 199.194 -0.531 44.037 1 29.8 ? O31 3PH 502 A 1 HETATM 18 C C31 3PH . . . M 13 199.643 -1.913 43.895 1 25.51 ? C31 3PH 502 A 1 HETATM 19 O O32 3PH . . . M 13 199.786 -2.415 42.795 1 25.78 ? O32 3PH 502 A 1 HETATM 20 C C32 3PH . . . M 13 199.929 -2.744 45.118 1 21.66 ? C32 3PH 502 A 1 HETATM 21 C C33 3PH . . . M 13 200.272 -4.178 44.726 1 16.61 ? C33 3PH 502 A 1 HETATM 22 C C34 3PH . . . M 13 199.944 -5.149 45.856 1 13.7 ? C34 3PH 502 A 1 HETATM 23 C C35 3PH . . . M 13 200.545 -6.504 45.504 1 20.12 ? C35 3PH 502 A 1 HETATM 24 C C36 3PH . . . M 13 200.88 -7.314 46.752 1 19.89 ? C36 3PH 502 A 1 HETATM 25 C C37 3PH . . . M 13 199.622 -7.872 47.416 1 23.29 ? C37 3PH 502 A 1 HETATM 26 C C38 3PH . . . M 13 199.993 -8.919 48.465 1 17.95 ? C38 3PH 502 A 1 HETATM 27 C C39 3PH . . . M 13 198.828 -9.861 48.726 1 15.72 ? C39 3PH 502 A 1 HETATM 28 C C3A 3PH . . . M 13 199.129 -10.698 49.963 1 19.14 ? C3A 3PH 502 A 1 HETATM 29 C C3B 3PH . . . M 13 199.112 -9.88 51.253 1 17.17 ? C3B 3PH 502 A 1 HETATM 30 C C3C 3PH . . . M 13 197.86 -10.224 52.058 1 16.42 ? C3C 3PH 502 A 1 HETATM 31 C C3D 3PH . . . M 13 198.012 -9.816 53.52 1 14.2 ? C3D 3PH 502 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #