data_8JD5
#
_model_server_result.job_id            lT2anaYVlvopb9CNrigmuA 
_model_server_result.datetime_utc      '2024-10-11 00:32:53' 
_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          8jd5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":904}' 
#
_entry.id    8JD5 
#
_exptl.entry_id    8JD5 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              691.959 
_entity.id                          10 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE 
_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            8JD5 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8JD5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      10 
_struct_asym.id                             J 
_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 42 2 CYS 50 1_555 A SG CYS 84 2 CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 A SG CYS 226 2 CYS 234 1_555 A SG CYS 510 2 CYS 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 347 2 CYS 355 1_555 A SG CYS 354 2 CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 A SG CYS 392 2 CYS 400 1_555 A SG CYS 399 2 CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 492 2 CYS 500 1_555 A SG CYS 511 2 CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf6 A SG CYS 496 2 CYS 504 1_555 A SG CYS 514 2 CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf7 A SG CYS 517 2 CYS 525 1_555 A SG CYS 529 2 CYS 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf8 A SG CYS 624 2 CYS 632 1_555 A SG CYS 713 2 CYS 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf9 B SG CYS 65 4 CYS 67 1_555 B SG CYS 107 4 CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf10 B SG CYS 247 4 CYS 249 1_555 B SG CYS 536 4 CYS 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf11 B SG CYS 426 4 CYS 428 1_555 B SG CYS 433 4 CYS 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf12 B SG CYS 518 4 CYS 520 1_555 B SG CYS 537 4 CYS 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf13 B SG CYS 522 4 CYS 524 1_555 B SG CYS 540 4 CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf14 B SG CYS 543 4 CYS 545 1_555 B SG CYS 555 4 CYS 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf15 B SG CYS 558 4 CYS 560 1_555 B SG CYS 571 4 CYS 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf16 B SG CYS 650 4 CYS 652 1_555 B SG CYS 744 4 CYS 746 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf17 F SG CYS 22 H CYS 22 1_555 F SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf18 F SG CYS 159 H CYS 159 1_555 F SG CYS 229 H CYS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A ND2 ASN 195 2 ASN 203 1_555 K C1 NAG . 2 NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale2 B ND2 ASN 452 4 ASN 454 1_555 P C1 NAG . 4 NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
#
_chem_comp.formula           'C37 H74 N O8 P' 
_chem_comp.formula_weight    691.959 
_chem_comp.id                PEF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-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
C2 C1 PEF sing 426 n n 
C2 C3 PEF sing 427 n n 
C2 O2 PEF sing 428 n n 
C2 H21 PEF sing 429 n n 
C1 O3P PEF sing 430 n n 
C1 H11 PEF sing 431 n n 
C1 H12 PEF sing 432 n n 
N C5 PEF sing 433 n n 
N HN1 PEF sing 434 n n 
N HN2 PEF sing 435 n n 
C3 O3 PEF sing 436 n n 
C3 H31 PEF sing 437 n n 
C3 H32 PEF sing 438 n n 
C4 C5 PEF sing 439 n n 
C4 O4P PEF sing 440 n n 
C4 H41 PEF sing 441 n n 
C4 H42 PEF sing 442 n n 
C5 H51 PEF sing 443 n n 
C5 H52 PEF sing 444 n n 
C10 C11 PEF sing 445 n n 
C10 O4 PEF doub 446 n n 
C10 O2 PEF sing 447 n n 
C11 C12 PEF sing 448 n n 
C11 H112 PEF sing 449 n n 
C11 H111 PEF sing 450 n n 
C12 C13 PEF sing 451 n n 
C12 H122 PEF sing 452 n n 
C12 H121 PEF sing 453 n n 
C13 C14 PEF sing 454 n n 
C13 H132 PEF sing 455 n n 
C13 H131 PEF sing 456 n n 
C14 C15 PEF sing 457 n n 
C14 H142 PEF sing 458 n n 
C14 H141 PEF sing 459 n n 
C15 C16 PEF sing 460 n n 
C15 H152 PEF sing 461 n n 
C15 H151 PEF sing 462 n n 
C16 C17 PEF sing 463 n n 
C16 H162 PEF sing 464 n n 
C16 H161 PEF sing 465 n n 
C17 C18 PEF sing 466 n n 
C17 H172 PEF sing 467 n n 
C17 H171 PEF sing 468 n n 
C18 C19 PEF sing 469 n n 
C18 H182 PEF sing 470 n n 
C18 H181 PEF sing 471 n n 
C19 C20 PEF sing 472 n n 
C19 H192 PEF sing 473 n n 
C19 H191 PEF sing 474 n n 
C20 C21 PEF sing 475 n n 
C20 H202 PEF sing 476 n n 
C20 H201 PEF sing 477 n n 
C21 C22 PEF sing 478 n n 
C21 H212 PEF sing 479 n n 
C21 H211 PEF sing 480 n n 
C22 C23 PEF sing 481 n n 
C22 H222 PEF sing 482 n n 
C22 H221 PEF sing 483 n n 
C23 C24 PEF sing 484 n n 
C23 H232 PEF sing 485 n n 
C23 H231 PEF sing 486 n n 
C24 C25 PEF sing 487 n n 
C24 H242 PEF sing 488 n n 
C24 H241 PEF sing 489 n n 
C25 H252 PEF sing 490 n n 
C25 H251 PEF sing 491 n n 
C25 H253 PEF sing 492 n n 
C30 C31 PEF sing 493 n n 
C30 O5 PEF doub 494 n n 
C30 O3 PEF sing 495 n n 
C31 C32 PEF sing 496 n n 
C31 H312 PEF sing 497 n n 
C31 H311 PEF sing 498 n n 
C32 C33 PEF sing 499 n n 
C32 H322 PEF sing 500 n n 
C32 H321 PEF sing 501 n n 
C33 C34 PEF sing 502 n n 
C33 H332 PEF sing 503 n n 
C33 H331 PEF sing 504 n n 
C34 C35 PEF sing 505 n n 
C34 H342 PEF sing 506 n n 
C34 H341 PEF sing 507 n n 
C35 C36 PEF sing 508 n n 
C35 H352 PEF sing 509 n n 
C35 H351 PEF sing 510 n n 
C36 C37 PEF sing 511 n n 
C36 H362 PEF sing 512 n n 
C36 H361 PEF sing 513 n n 
C37 C38 PEF sing 514 n n 
C37 H372 PEF sing 515 n n 
C37 H371 PEF sing 516 n n 
C38 C39 PEF sing 517 n n 
C38 H382 PEF sing 518 n n 
C38 H381 PEF sing 519 n n 
C39 C40 PEF sing 520 n n 
C39 H392 PEF sing 521 n n 
C39 H391 PEF sing 522 n n 
C40 C41 PEF sing 523 n n 
C40 H402 PEF sing 524 n n 
C40 H401 PEF sing 525 n n 
C41 C42 PEF sing 526 n n 
C41 H412 PEF sing 527 n n 
C41 H411 PEF sing 528 n n 
C42 C43 PEF sing 529 n n 
C42 H422 PEF sing 530 n n 
C42 H421 PEF sing 531 n n 
C43 C44 PEF sing 532 n n 
C43 H432 PEF sing 533 n n 
C43 H431 PEF sing 534 n n 
C44 C45 PEF sing 535 n n 
C44 H442 PEF sing 536 n n 
C44 H441 PEF sing 537 n n 
C45 H452 PEF sing 538 n n 
C45 H451 PEF sing 539 n n 
C45 H453 PEF sing 540 n n 
O1P P PEF doub 541 n n 
O2P P PEF sing 542 n n 
O2P HOP2 PEF sing 543 n n 
O3P P PEF sing 544 n n 
O4P P PEF sing 545 n n 
#
_atom_sites.entry_id                     8JD5 
_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
G 7 HZR 2 1 901 901 HZR JNJ . 
H 8 GLU 2 1 902 902 GLU GLA . 
I 9 CLR 2 1 903 904 CLR CLR . 
J 10 PEF 2 1 904 1006 PEF LIP . 
K 11 NAG 2 1 905 2001 NAG NAG . 
L 9 CLR 2 1 906 2101 CLR CLR . 
M 9 CLR 2 1 907 2201 CLR CLR . 
N 9 CLR 4 1 1001 903 CLR CLR . 
O 8 GLU 4 1 1002 901 GLU GLA . 
P 11 NAG 4 1 1003 2001 NAG NAG . 
Q 12 BQI 4 1 1004 2101 BQI ADX . 
R 9 CLR 4 1 1005 2102 CLR CLR . 
#
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 C2 PEF . . . J 10 192.443 210.03 161.77 1 66.02 ? C2 PEF 904 2 1 
HETATM 2 C C1 PEF . . . J 10 191.969 210.481 160.359 1 66.02 ? C1 PEF 904 2 1 
HETATM 3 N N PEF . . . J 10 192.802 212.958 155.791 1 66.02 ? N PEF 904 2 1 
HETATM 4 C C3 PEF . . . J 10 192.233 211.122 162.856 1 66.02 ? C3 PEF 904 2 1 
HETATM 5 C C4 PEF . . . J 10 190.991 212.301 157.362 1 66.02 ? C4 PEF 904 2 1 
HETATM 6 C C5 PEF . . . J 10 191.715 211.991 156.019 1 66.02 ? C5 PEF 904 2 1 
HETATM 7 C C10 PEF . . . J 10 192.454 207.724 162.564 1 66.02 ? C10 PEF 904 2 1 
HETATM 8 C C11 PEF . . . J 10 193.805 207.922 163.356 1 66.02 ? C11 PEF 904 2 1 
HETATM 9 C C12 PEF . . . J 10 194.599 206.586 163.479 1 66.02 ? C12 PEF 904 2 1 
HETATM 10 C C13 PEF . . . J 10 194.151 205.76 164.731 1 66.02 ? C13 PEF 904 2 1 
HETATM 11 C C14 PEF . . . J 10 194.812 206.265 166.028 1 66.02 ? C14 PEF 904 2 1 
HETATM 12 C C15 PEF . . . J 10 193.884 206.113 167.263 1 66.02 ? C15 PEF 904 2 1 
HETATM 13 C C16 PEF . . . J 10 194.562 206.65 168.567 1 66.02 ? C16 PEF 904 2 1 
HETATM 14 C C17 PEF . . . J 10 196.106 206.455 168.533 1 66.02 ? C17 PEF 904 2 1 
HETATM 15 C C18 PEF . . . J 10 196.658 205.874 169.887 1 66.02 ? C18 PEF 904 2 1 
HETATM 16 C C19 PEF . . . J 10 195.735 204.763 170.453 1 66.02 ? C19 PEF 904 2 1 
HETATM 17 C C20 PEF . . . J 10 196.243 204.241 171.833 1 66.02 ? C20 PEF 904 2 1 
HETATM 18 C C21 PEF . . . J 10 195.707 205.09 173.012 1 66.02 ? C21 PEF 904 2 1 
HETATM 19 C C22 PEF . . . J 10 196.646 204.998 174.244 1 66.02 ? C22 PEF 904 2 1 
HETATM 20 C C23 PEF . . . J 10 196.402 206.128 175.283 1 66.02 ? C23 PEF 904 2 1 
HETATM 21 C C24 PEF . . . J 10 196.927 205.727 176.692 1 66.02 ? C24 PEF 904 2 1 
HETATM 22 C C25 PEF . . . J 10 197.954 206.738 177.252 1 66.02 ? C25 PEF 904 2 1 
HETATM 23 C C30 PEF . . . J 10 191.04 211.192 164.894 1 66.02 ? C30 PEF 904 2 1 
HETATM 24 C C31 PEF . . . J 10 190.009 210.549 165.864 1 66.02 ? C31 PEF 904 2 1 
HETATM 25 C C32 PEF . . . J 10 190.646 209.478 166.775 1 66.02 ? C32 PEF 904 2 1 
HETATM 26 C C33 PEF . . . J 10 191.459 210.086 167.965 1 66.02 ? C33 PEF 904 2 1 
HETATM 27 C C34 PEF . . . J 10 191.688 209.058 169.091 1 66.02 ? C34 PEF 904 2 1 
HETATM 28 C C35 PEF . . . J 10 192.801 209.478 170.092 1 66.02 ? C35 PEF 904 2 1 
HETATM 29 C C36 PEF . . . J 10 193.084 211.019 170.093 1 66.02 ? C36 PEF 904 2 1 
HETATM 30 C C37 PEF . . . J 10 194.586 211.363 170.177 1 66.02 ? C37 PEF 904 2 1 
HETATM 31 C C38 PEF . . . J 10 195.527 210.15 169.766 1 66.02 ? C38 PEF 904 2 1 
HETATM 32 C C39 PEF . . . J 10 197.042 210.518 169.832 1 66.02 ? C39 PEF 904 2 1 
HETATM 33 C C40 PEF . . . J 10 197.482 211.079 171.23 1 66.02 ? C40 PEF 904 2 1 
HETATM 34 C C41 PEF . . . J 10 197.326 210.031 172.371 1 66.02 ? C41 PEF 904 2 1 
HETATM 35 C C42 PEF . . . J 10 197.934 210.53 173.707 1 66.02 ? C42 PEF 904 2 1 
HETATM 36 C C43 PEF . . . J 10 198.288 209.355 174.665 1 66.02 ? C43 PEF 904 2 1 
HETATM 37 C C44 PEF . . . J 10 199.335 209.749 175.747 1 66.02 ? C44 PEF 904 2 1 
HETATM 38 C C45 PEF . . . J 10 200.33 210.833 175.254 1 66.02 ? C45 PEF 904 2 1 
HETATM 39 O O4 PEF . . . J 10 192.079 206.626 162.316 1 66.02 ? O4 PEF 904 2 1 
HETATM 40 O O5 PEF . . . J 10 191.872 211.928 165.315 1 66.02 ? O5 PEF 904 2 1 
HETATM 41 O O2 PEF . . . J 10 191.664 208.869 162.148 1 66.02 ? O2 PEF 904 2 1 
HETATM 42 O O3 PEF . . . J 10 190.996 210.898 163.508 1 66.02 ? O3 PEF 904 2 1 
HETATM 43 O O1P PEF . . . J 10 188.213 210.528 159.307 1 66.02 -1 O1P PEF 904 2 1 
HETATM 44 O O2P PEF . . . J 10 189.635 212.446 159.914 1 66.02 ? O2P PEF 904 2 1 
HETATM 45 O O3P PEF . . . J 10 190.633 210.065 160.153 1 66.02 ? O3P PEF 904 2 1 
HETATM 46 O O4P PEF . . . J 10 190.175 211.188 157.708 1 66.02 ? O4P PEF 904 2 1 
HETATM 47 P P PEF . . . J 10 189.626 211.075 159.286 1 66.02 ? P PEF 904 2 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           47 
#