data_8IB7
#
_model_server_result.job_id            wZUx4qsEXqPD_bvVH_bmGQ 
_model_server_result.datetime_utc      '2024-10-19 20:19:37' 
_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          8ib7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"NA","auth_seq_id":402}' 
#
_entry.id    8IB7 
#
_exptl.entry_id    8IB7 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              704.998 
_entity.id                          17 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    21-meric 
_pdbx_struct_assembly.oligomeric_count      21 
_pdbx_struct_assembly.details               author_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,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    ? 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 17 CA N N 
? 17 NA 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 A SG CYS 338 AA CYS 338 1_555 A SG CYS 360 AA CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
disulf ? disulf2 E SG CYS 222 AE CYS 222 1_555 E SG CYS 238 AE CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf3 H SG CYS 51 AH CYS 51 1_555 H SG CYS 65 AH CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 L SG CYS 338 Aa CYS 338 1_555 L SG CYS 360 Aa CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 P SG CYS 222 Ae CYS 222 1_555 P SG CYS 238 Ae CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf6 S SG CYS 35 Ah CYS 35 1_555 S SG CYS 79 Ah CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf7 S SG CYS 51 Ah CYS 51 1_555 S SG CYS 65 Ah CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 C NE2 HIS 83 AC HIS 83 1_555 V FE HEM . AC HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? 
metalc ? metalc2 C NE2 HIS 97 AC HIS 97 1_555 W FE HEM . AC HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc3 C NE2 HIS 182 AC HIS 182 1_555 V FE HEM . AC HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc4 C NE2 HIS 196 AC HIS 196 1_555 W FE HEM . AC HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc5 D NE2 HIS 125 AD HIS 125 1_555 BA FE HEC . AD HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc6 D SD MET 244 AD MET 244 1_555 BA FE HEC . AD HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc7 N NE2 HIS 83 Ac HIS 83 1_555 GA FE HEM . Ac HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc8 N NE2 HIS 97 Ac HIS 97 1_555 HA FE HEM . Ac HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.775 ? 
metalc ? metalc9 N NE2 HIS 182 Ac HIS 182 1_555 GA FE HEM . Ac HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc10 N NE2 HIS 196 Ac HIS 196 1_555 HA FE HEM . Ac HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? 
metalc ? metalc11 O NE2 HIS 125 Ad HIS 125 1_555 MA FE HEC . Ad HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc12 O SD MET 244 Ad MET 244 1_555 MA FE HEC . Ad HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
#
_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                     8IB7 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
V 11 HEM AC 1 401 401 HEM HEM . 
W 11 HEM AC 1 402 402 HEM HEM . 
X 12 3PE AC 1 403 403 3PE 3PE . 
Y 13 U10 AC 1 404 505 U10 U10 . 
Z 14 UQ6 AC 1 405 506 UQ6 UQ6 . 
AA 15 CDL AC 1 406 103 CDL CDL . 
BA 16 HEC AD 1 401 395 HEC HEC . 
CA 17 3PH AD 1 402 400 3PH 3PH . 
DA 12 3PE AF 1 201 104 3PE 3PE . 
EA 15 CDL Aa 1 501 536 CDL CDL . 
FA 12 3PE Ac 1 401 535 3PE 3PE . 
GA 11 HEM Ac 1 402 401 HEM HEM . 
HA 11 HEM Ac 1 403 402 HEM HEM . 
IA 12 3PE Ac 1 404 403 3PE 3PE . 
JA 13 U10 Ac 1 405 505 U10 U10 . 
KA 14 UQ6 Ac 1 406 506 UQ6 UQ6 . 
LA 15 CDL Ac 1 407 102 CDL CDL . 
MA 16 HEC Ad 1 401 395 HEC HEC . 
NA 17 3PH Ad 1 402 400 3PH 3PH . 
OA 15 CDL Ag 1 101 103 CDL CDL . 
PA 12 3PE Ag 1 102 104 3PE 3PE . 
#
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 . . . NA 17 130.996 197.235 190.142 1 62.69 -1 O13 3PH 402 Ad 1 
HETATM 2 P P 3PH . . . NA 17 131.338 196.487 191.405 1 61.6 0 P 3PH 402 Ad 1 
HETATM 3 O O14 3PH . . . NA 17 131.389 197.349 192.64 1 62.9 0 O14 3PH 402 Ad 1 
HETATM 4 O O12 3PH . . . NA 17 130.601 195.184 191.584 1 63.19 0 O12 3PH 402 Ad 1 
HETATM 5 O O11 3PH . . . NA 17 132.865 196.035 191.189 1 62.24 0 O11 3PH 402 Ad 1 
HETATM 6 C C1 3PH . . . NA 17 133.445 195.085 192.074 1 59 0 C1 3PH 402 Ad 1 
HETATM 7 C C2 3PH . . . NA 17 134.778 195.609 192.584 1 56.98 0 C2 3PH 402 Ad 1 
HETATM 8 O O21 3PH . . . NA 17 135.227 194.757 193.626 1 54.49 0 O21 3PH 402 Ad 1 
HETATM 9 C C21 3PH . . . NA 17 136.344 193.943 193.192 1 51.1 0 C21 3PH 402 Ad 1 
HETATM 10 O O22 3PH . . . NA 17 137.439 194.455 193.034 1 51.27 0 O22 3PH 402 Ad 1 
HETATM 11 C C22 3PH . . . NA 17 136.119 192.478 192.933 1 48.84 0 C22 3PH 402 Ad 1 
HETATM 12 C C23 3PH . . . NA 17 137.413 191.698 193.118 1 47.14 0 C23 3PH 402 Ad 1 
HETATM 13 C C24 3PH . . . NA 17 137.961 191.825 194.537 1 46.8 0 C24 3PH 402 Ad 1 
HETATM 14 C C25 3PH . . . NA 17 139.139 190.882 194.763 1 46.97 0 C25 3PH 402 Ad 1 
HETATM 15 C C26 3PH . . . NA 17 140.04 191.383 195.886 1 47.77 0 C26 3PH 402 Ad 1 
HETATM 16 C C27 3PH . . . NA 17 141.42 190.731 195.869 1 48.91 0 C27 3PH 402 Ad 1 
HETATM 17 C C28 3PH . . . NA 17 141.526 189.52 196.788 1 50.06 0 C28 3PH 402 Ad 1 
HETATM 18 C C29 3PH . . . NA 17 140.739 188.325 196.265 1 49.58 0 C29 3PH 402 Ad 1 
HETATM 19 C C2A 3PH . . . NA 17 140.846 187.143 197.22 1 49.07 0 C2A 3PH 402 Ad 1 
HETATM 20 C C2B 3PH . . . NA 17 139.998 185.973 196.738 1 47.98 0 C2B 3PH 402 Ad 1 
HETATM 21 C C2C 3PH . . . NA 17 140.015 184.833 197.747 1 47.53 0 C2C 3PH 402 Ad 1 
HETATM 22 C C3 3PH . . . NA 17 134.593 197.004 193.157 1 57.1 0 C3 3PH 402 Ad 1 
HETATM 23 O O31 3PH . . . NA 17 135.504 197.193 194.236 1 56.92 0 O31 3PH 402 Ad 1 
HETATM 24 C C31 3PH . . . NA 17 136.932 197.258 193.979 1 56.89 0 C31 3PH 402 Ad 1 
HETATM 25 O O32 3PH . . . NA 17 137.338 197.318 192.832 1 58.14 0 O32 3PH 402 Ad 1 
HETATM 26 C C32 3PH . . . NA 17 137.9 197.247 195.13 1 56.09 0 C32 3PH 402 Ad 1 
HETATM 27 C C33 3PH . . . NA 17 137.826 195.89 195.81 1 53.91 0 C33 3PH 402 Ad 1 
HETATM 28 C C34 3PH . . . NA 17 138.738 195.88 197.023 1 52.72 0 C34 3PH 402 Ad 1 
HETATM 29 C C35 3PH . . . NA 17 140.19 196.136 196.651 1 53.39 0 C35 3PH 402 Ad 1 
HETATM 30 C C36 3PH . . . NA 17 141.017 196.289 197.918 1 54.27 0 C36 3PH 402 Ad 1 
HETATM 31 C C37 3PH . . . NA 17 140.86 195.068 198.812 1 55.87 0 C37 3PH 402 Ad 1 
HETATM 32 C C38 3PH . . . NA 17 141.515 193.833 198.209 1 58.18 0 C38 3PH 402 Ad 1 
HETATM 33 C C39 3PH . . . NA 17 141.134 192.579 198.987 1 58.68 0 C39 3PH 402 Ad 1 
HETATM 34 C C3A 3PH . . . NA 17 141.388 192.745 200.48 1 58.66 0 C3A 3PH 402 Ad 1 
HETATM 35 C C3B 3PH . . . NA 17 142.851 193.059 200.761 1 58.23 0 C3B 3PH 402 Ad 1 
HETATM 36 C C3C 3PH . . . NA 17 143.125 193.116 202.258 1 58.24 0 C3C 3PH 402 Ad 1 
#
_model_server_stats.io_time_ms              113 
_model_server_stats.parse_time_ms           101 
_model_server_stats.create_model_time_ms    129 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           36 
#