data_7XJD
#
_model_server_result.job_id            VNpkAVjP3I5YlW_MN3JJKg 
_model_server_result.datetime_utc      '2024-11-21 14:16:05' 
_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          7xjd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":313}' 
#
_entry.id    7XJD 
#
_exptl.entry_id    7XJD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              653.157 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2,3-DI-PHYTANYL-GLYCEROL 
_entity.pdbx_number_of_molecules    14 
_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            7XJD 
_cell.length_a            60.57 
_cell.length_b            60.57 
_cell.length_c            110.89 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7XJD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_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,L,M,N,O,P,Q,R,S,T,U 
_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_635 -y+1,x-y-2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 121.14 -104.910317 0 
3 'crystal symmetry operation' 3_865 -x+y+3,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 151.425 52.455159 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 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 P N N 
? 3 Q 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             212 
_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              301 
_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        ? 
_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                1.351 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C43 H88 O3' 
_chem_comp.formula_weight    653.157 
_chem_comp.id                L2P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2,3-DI-PHYTANYL-GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL 
#
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 O1 L2P sing 139 n n 
C1 C2 L2P sing 140 n n 
C1 H12 L2P sing 141 n n 
C1 H11 L2P sing 142 n n 
O1 C11 L2P sing 143 n n 
C2 O2 L2P sing 144 n n 
C2 C3 L2P sing 145 n n 
C2 H2 L2P sing 146 n n 
O2 C41 L2P sing 147 n n 
C3 O3 L2P sing 148 n n 
C3 H32 L2P sing 149 n n 
C3 H31 L2P sing 150 n n 
O3 H3O L2P sing 151 n n 
C11 C12 L2P sing 152 n n 
C11 H112 L2P sing 153 n n 
C11 H111 L2P sing 154 n n 
C12 C13 L2P sing 155 n n 
C12 H122 L2P sing 156 n n 
C12 H121 L2P sing 157 n n 
C13 C14 L2P sing 158 n n 
C13 C15 L2P sing 159 n n 
C13 H13 L2P sing 160 n n 
C14 H143 L2P sing 161 n n 
C14 H142 L2P sing 162 n n 
C14 H141 L2P sing 163 n n 
C15 C16 L2P sing 164 n n 
C15 H152 L2P sing 165 n n 
C15 H151 L2P sing 166 n n 
C16 C17 L2P sing 167 n n 
C16 H162 L2P sing 168 n n 
C16 H161 L2P sing 169 n n 
C17 C18 L2P sing 170 n n 
C17 H172 L2P sing 171 n n 
C17 H171 L2P sing 172 n n 
C18 C19 L2P sing 173 n n 
C18 C20 L2P sing 174 n n 
C18 H18 L2P sing 175 n n 
C19 H193 L2P sing 176 n n 
C19 H192 L2P sing 177 n n 
C19 H191 L2P sing 178 n n 
C20 C21 L2P sing 179 n n 
C20 H202 L2P sing 180 n n 
C20 H201 L2P sing 181 n n 
C21 C22 L2P sing 182 n n 
C21 H212 L2P sing 183 n n 
C21 H211 L2P sing 184 n n 
C22 C23 L2P sing 185 n n 
C22 H222 L2P sing 186 n n 
C22 H221 L2P sing 187 n n 
C23 C24 L2P sing 188 n n 
C23 C25 L2P sing 189 n n 
C23 H23 L2P sing 190 n n 
C24 H243 L2P sing 191 n n 
C24 H242 L2P sing 192 n n 
C24 H241 L2P sing 193 n n 
C25 C26 L2P sing 194 n n 
C25 H252 L2P sing 195 n n 
C25 H251 L2P sing 196 n n 
C26 C27 L2P sing 197 n n 
C26 H262 L2P sing 198 n n 
C26 H261 L2P sing 199 n n 
C27 C28 L2P sing 200 n n 
C27 H272 L2P sing 201 n n 
C27 H271 L2P sing 202 n n 
C28 C29 L2P sing 203 n n 
C28 C30 L2P sing 204 n n 
C28 H28 L2P sing 205 n n 
C29 H293 L2P sing 206 n n 
C29 H292 L2P sing 207 n n 
C29 H291 L2P sing 208 n n 
C30 H303 L2P sing 209 n n 
C30 H302 L2P sing 210 n n 
C30 H301 L2P sing 211 n n 
C41 C42 L2P sing 212 n n 
C41 H412 L2P sing 213 n n 
C41 H411 L2P sing 214 n n 
C42 C43 L2P sing 215 n n 
C42 H422 L2P sing 216 n n 
C42 H421 L2P sing 217 n n 
C43 C44 L2P sing 218 n n 
C43 C45 L2P sing 219 n n 
C43 H43 L2P sing 220 n n 
C44 H443 L2P sing 221 n n 
C44 H442 L2P sing 222 n n 
C44 H441 L2P sing 223 n n 
C45 C46 L2P sing 224 n n 
C45 H452 L2P sing 225 n n 
C45 H451 L2P sing 226 n n 
C46 C47 L2P sing 227 n n 
C46 H462 L2P sing 228 n n 
C46 H461 L2P sing 229 n n 
C47 C48 L2P sing 230 n n 
C47 H472 L2P sing 231 n n 
C47 H471 L2P sing 232 n n 
C48 C49 L2P sing 233 n n 
C48 C50 L2P sing 234 n n 
C48 H48 L2P sing 235 n n 
C49 H493 L2P sing 236 n n 
C49 H492 L2P sing 237 n n 
C49 H491 L2P sing 238 n n 
C50 C51 L2P sing 239 n n 
C50 H502 L2P sing 240 n n 
C50 H501 L2P sing 241 n n 
C51 C52 L2P sing 242 n n 
C51 H512 L2P sing 243 n n 
C51 H511 L2P sing 244 n n 
C52 C53 L2P sing 245 n n 
C52 H522 L2P sing 246 n n 
C52 H521 L2P sing 247 n n 
C53 C54 L2P sing 248 n n 
C53 C55 L2P sing 249 n n 
C53 H53 L2P sing 250 n n 
C54 H543 L2P sing 251 n n 
C54 H542 L2P sing 252 n n 
C54 H541 L2P sing 253 n n 
C55 C56 L2P sing 254 n n 
C55 H552 L2P sing 255 n n 
C55 H551 L2P sing 256 n n 
C56 C57 L2P sing 257 n n 
C56 H562 L2P sing 258 n n 
C56 H561 L2P sing 259 n n 
C57 C58 L2P sing 260 n n 
C57 H572 L2P sing 261 n n 
C57 H571 L2P sing 262 n n 
C58 C59 L2P sing 263 n n 
C58 C60 L2P sing 264 n n 
C58 H58 L2P sing 265 n n 
C59 H593 L2P sing 266 n n 
C59 H592 L2P sing 267 n n 
C59 H591 L2P sing 268 n n 
C60 H603 L2P sing 269 n n 
C60 H602 L2P sing 270 n n 
C60 H601 L2P sing 271 n n 
#
_atom_sites.entry_id                     7XJD 
_atom_sites.fract_transf_matrix[1][1]    0.01651 
_atom_sites.fract_transf_matrix[1][2]    0.009532 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019064 
_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]    0.009018 
_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 1 301 301 RET RET . 
C 3 L2P A 1 302 302 L2P L2P . 
D 3 L2P A 1 303 303 L2P L2P . 
E 3 L2P A 1 304 304 L2P L2P . 
F 3 L2P A 1 305 305 L2P L2P . 
G 3 L2P A 1 306 306 L2P L2P . 
H 4 SQU A 1 312 312 SQU SQU . 
I 3 L2P A 1 313 313 L2P L2P . 
J 3 L2P A 1 315 315 L2P L2P . 
K 3 L2P A 1 320 320 L2P L2P . 
L 3 L2P A 1 322 322 L2P L2P . 
M 3 L2P A 1 323 323 L2P L2P . 
N 3 L2P A 1 324 324 L2P L2P . 
O 3 L2P A 1 327 327 L2P L2P . 
P 3 L2P A 1 328 328 L2P L2P . 
Q 3 L2P A 1 333 333 L2P L2P . 
R 4 SQU A 1 341 341 SQU SQU . 
S 4 SQU A 1 342 342 SQU SQU . 
T 4 SQU A 1 343 343 SQU SQU . 
U 5 HOH A 1 401 401 HOH HOH . 
U 5 HOH A 2 402 402 HOH HOH . 
U 5 HOH A 3 403 403 HOH HOH . 
U 5 HOH A 4 404 404 HOH HOH . 
U 5 HOH A 5 405 405 HOH HOH . 
U 5 HOH A 6 406 406 HOH HOH . 
U 5 HOH A 7 407 407 HOH HOH . 
U 5 HOH A 8 411 411 HOH HOH . 
U 5 HOH A 9 412 412 HOH HOH . 
U 5 HOH A 10 415 415 HOH HOH . 
U 5 HOH A 11 416 416 HOH HOH . 
U 5 HOH A 12 419 419 HOH HOH . 
U 5 HOH A 13 420 420 HOH HOH . 
U 5 HOH A 14 450 450 HOH HOH . 
U 5 HOH A 15 451 451 HOH HOH . 
U 5 HOH A 16 453 453 HOH HOH . 
U 5 HOH A 17 454 454 HOH HOH . 
U 5 HOH A 18 455 455 HOH HOH . 
U 5 HOH A 19 456 456 HOH HOH . 
U 5 HOH A 20 457 457 HOH HOH . 
U 5 HOH A 21 458 458 HOH HOH . 
U 5 HOH A 22 459 459 HOH HOH . 
U 5 HOH A 23 460 460 HOH HOH . 
U 5 HOH A 24 501 501 HOH HOH . 
U 5 HOH A 25 502 502 HOH HOH . 
U 5 HOH A 26 511 511 HOH HOH . 
U 5 HOH A 27 512 512 HOH HOH . 
U 5 HOH A 28 513 513 HOH HOH . 
U 5 HOH A 29 514 514 HOH HOH . 
U 5 HOH A 30 530 530 HOH HOH . 
U 5 HOH A 31 531 531 HOH HOH . 
U 5 HOH A 32 532 532 HOH HOH . 
U 5 HOH A 33 533 533 HOH HOH . 
U 5 HOH A 34 534 534 HOH HOH . 
U 5 HOH A 35 535 535 HOH HOH . 
U 5 HOH A 36 536 536 HOH HOH . 
U 5 HOH A 37 537 537 HOH HOH . 
U 5 HOH A 38 538 538 HOH HOH . 
U 5 HOH A 39 539 539 HOH HOH . 
U 5 HOH A 40 540 540 HOH HOH . 
U 5 HOH A 41 541 541 HOH HOH . 
U 5 HOH A 42 542 542 HOH HOH . 
U 5 HOH A 43 543 543 HOH HOH . 
U 5 HOH A 44 544 544 HOH HOH . 
U 5 HOH A 45 545 545 HOH HOH . 
U 5 HOH A 46 546 546 HOH HOH . 
U 5 HOH A 47 547 547 HOH HOH . 
U 5 HOH A 48 548 548 HOH HOH . 
U 5 HOH A 49 549 549 HOH HOH . 
U 5 HOH A 50 550 550 HOH HOH . 
U 5 HOH A 51 551 551 HOH HOH . 
U 5 HOH A 52 552 552 HOH HOH . 
U 5 HOH A 53 553 553 HOH HOH . 
U 5 HOH A 54 554 554 HOH HOH . 
U 5 HOH A 55 555 555 HOH HOH . 
U 5 HOH A 56 556 556 HOH HOH . 
U 5 HOH A 57 557 557 HOH HOH . 
U 5 HOH A 58 558 558 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 L2P . . . I 3 62.794 -36.349 -34.88 1 72.91 ? C1 L2P 313 A 1 
HETATM 2 O O1 L2P . . . I 3 63.225 -36.987 -33.652 1 72.9 ? O1 L2P 313 A 1 
HETATM 3 C C2 L2P . . . I 3 63.845 -35.767 -35.842 1 73 ? C2 L2P 313 A 1 
HETATM 4 O O2 L2P . . . I 3 64.818 -34.822 -35.306 1 73.08 ? O2 L2P 313 A 1 
HETATM 5 C C11 L2P . . . I 3 62.582 -37.008 -32.352 1 72.66 ? C11 L2P 313 A 1 
HETATM 6 C C12 L2P . . . I 3 62.31 -38.318 -31.609 1 72.44 ? C12 L2P 313 A 1 
HETATM 7 C C13 L2P . . . I 3 61.231 -38.256 -30.53 1 72.31 ? C13 L2P 313 A 1 
HETATM 8 C C14 L2P . . . I 3 60.752 -36.866 -30.108 1 71.88 ? C14 L2P 313 A 1 
HETATM 9 C C41 L2P . . . I 3 65.102 -34.617 -33.894 1 73.06 ? C41 L2P 313 A 1 
HETATM 10 C C42 L2P . . . I 3 66.506 -34.375 -33.351 1 73.14 ? C42 L2P 313 A 1 
HETATM 11 C C43 L2P . . . I 3 66.762 -34.751 -31.901 1 73.23 ? C43 L2P 313 A 1 
HETATM 12 C C44 L2P . . . I 3 67.265 -36.151 -31.586 1 73.24 ? C44 L2P 313 A 1 
HETATM 13 C C45 L2P . . . I 3 66.161 -33.9 -30.796 1 73.29 ? C45 L2P 313 A 1 
HETATM 14 C C46 L2P . . . I 3 66.567 -34.222 -29.36 1 73.39 ? C46 L2P 313 A 1 
HETATM 15 C C47 L2P . . . I 3 65.873 -35.411 -28.689 1 73.57 ? C47 L2P 313 A 1 
HETATM 16 C C48 L2P . . . I 3 66.749 -36.438 -27.974 1 73.64 ? C48 L2P 313 A 1 
HETATM 17 C C49 L2P . . . I 3 66.583 -36.64 -26.467 1 73.76 ? C49 L2P 313 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           249 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           17 
#