data_4PD4
#
_model_server_result.job_id            -5V0VaWvYp3s31O_ENGqPw 
_model_server_result.datetime_utc      '2025-06-20 13:51:44' 
_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":"S","auth_seq_id":4006}' 
#
_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 . . . S 13 216.664 1.477 69.276 1 29.68 ? O13 3PH 4006 C 1 
HETATM 2 P P 3PH . . . S 13 215.846 1.847 70.477 1 39.14 ? P 3PH 4006 C 1 
HETATM 3 O O14 3PH . . . S 13 216.577 2.215 71.776 1 30.38 ? O14 3PH 4006 C 1 
HETATM 4 O O12 3PH . . . S 13 214.642 2.783 70.247 1 20.7 ? O12 3PH 4006 C 1 
HETATM 5 O O11 3PH . . . S 13 215.277 0.429 70.953 1 25.7 ? O11 3PH 4006 C 1 
HETATM 6 C C1 3PH . . . S 13 216.172 -0.426 71.636 1 20.24 ? C1 3PH 4006 C 1 
HETATM 7 C C2 3PH . . . S 13 215.595 -1.835 71.579 1 25.66 ? C2 3PH 4006 C 1 
HETATM 8 O O21 3PH . . . S 13 216.166 -2.613 70.5 1 28.48 ? O21 3PH 4006 C 1 
HETATM 9 C C21 3PH . . . S 13 217.237 -3.489 70.963 1 22.34 ? C21 3PH 4006 C 1 
HETATM 10 O O22 3PH . . . S 13 217.901 -3.127 71.918 1 17 ? O22 3PH 4006 C 1 
HETATM 11 C C22 3PH . . . S 13 217.524 -4.798 70.274 1 19.11 ? C22 3PH 4006 C 1 
HETATM 12 C C23 3PH . . . S 13 216.467 -5.811 70.66 1 19.29 ? C23 3PH 4006 C 1 
HETATM 13 C C24 3PH . . . S 13 216.969 -7.206 70.347 1 23.18 ? C24 3PH 4006 C 1 
HETATM 14 C C25 3PH . . . S 13 216.022 -8.286 70.851 1 25.16 ? C25 3PH 4006 C 1 
HETATM 15 C C3 3PH . . . S 13 214.088 -1.67 71.372 1 19.18 ? C3 3PH 4006 C 1 
HETATM 16 O O31 3PH . . . S 13 213.575 -2.854 70.79 1 17.83 ? O31 3PH 4006 C 1 
HETATM 17 C C31 3PH . . . S 13 212.653 -3.663 71.582 1 20.5 ? C31 3PH 4006 C 1 
HETATM 18 O O32 3PH . . . S 13 212.072 -3.183 72.542 1 19.85 ? O32 3PH 4006 C 1 
HETATM 19 C C32 3PH . . . S 13 212.432 -5.105 71.231 1 14.23 ? C32 3PH 4006 C 1 
HETATM 20 C C33 3PH . . . S 13 211.751 -5.838 72.36 1 13.6 ? C33 3PH 4006 C 1 
HETATM 21 C C34 3PH . . . S 13 212.635 -7.03 72.679 1 17.15 ? C34 3PH 4006 C 1 
HETATM 22 C C35 3PH . . . S 13 211.815 -8.274 73.006 1 17.26 ? C35 3PH 4006 C 1 
HETATM 23 C C36 3PH . . . S 13 211.756 -9.234 71.824 1 12.23 ? C36 3PH 4006 C 1 
HETATM 24 C C37 3PH . . . S 13 210.649 -10.229 72.113 1 10.39 ? C37 3PH 4006 C 1 
HETATM 25 C C38 3PH . . . S 13 211.139 -11.325 73.038 1 10.55 ? C38 3PH 4006 C 1 
HETATM 26 C C39 3PH . . . S 13 209.944 -12.067 73.605 1 10.7 ? C39 3PH 4006 C 1 
HETATM 27 C C3A 3PH . . . S 13 209.311 -11.221 74.698 1 9.51 ? C3A 3PH 4006 C 1 
HETATM 28 C C3B 3PH . . . S 13 209.278 -12.125 75.916 1 10 ? C3B 3PH 4006 C 1 
HETATM 29 C C3C 3PH . . . S 13 207.859 -12.344 76.354 1 8.17 ? C3C 3PH 4006 C 1 
HETATM 30 C C3D 3PH . . . S 13 207.285 -11.071 76.917 1 3.37 ? C3D 3PH 4006 C 1 
HETATM 31 C C3E 3PH . . . S 13 206.124 -11.686 77.635 1 3.68 ? C3E 3PH 4006 C 1 
HETATM 32 C C3F 3PH . . . S 13 205.566 -10.74 78.654 1 5.6 ? C3F 3PH 4006 C 1 
HETATM 33 C C3G 3PH . . . S 13 205.171 -11.568 79.862 1 7.2 ? C3G 3PH 4006 C 1 
HETATM 34 C C3H 3PH . . . S 13 204.281 -12.733 79.495 1 6.9 ? C3H 3PH 4006 C 1 
HETATM 35 C C3I 3PH . . . S 13 202.908 -12.197 79.133 1 9.89 ? C3I 3PH 4006 C 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           35 
#