data_3EKD
#
_model_server_result.job_id            PZQXXGq46ekzwV4Q1DwXZQ 
_model_server_result.datetime_utc      '2025-06-20 10:09:33' 
_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          3ekd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":471}' 
#
_entry.id    3EKD 
#
_exptl.entry_id    3EKD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              254.408 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PALMITOLEIC ACID' 
_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            3EKD 
_cell.length_a            63.769 
_cell.length_b            125.171 
_cell.length_c            153.943 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EKD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,F 1 1 
B,E,G 2 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    x,y,z 
_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                      2 
_struct_asym.id                             C 
_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
metalc ? metalc1 A SG CYS 400 A CYS 400 1_555 D FE HEM . A HEM 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
metalc ? metalc2 B SG CYS 400 B CYS 400 1_555 E FE HEM . B HEM 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
#
_chem_comp.formula           'C16 H30 O2' 
_chem_comp.formula_weight    254.408 
_chem_comp.id                PAM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PALMITOLEIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 PAM sing 319 n n 
C1 O2 PAM doub 320 n n 
C1 C2 PAM sing 321 n n 
O1 HO1 PAM sing 322 n n 
C2 C3 PAM sing 323 n n 
C2 H21 PAM sing 324 n n 
C2 H22 PAM sing 325 n n 
C3 C4 PAM sing 326 n n 
C3 H31 PAM sing 327 n n 
C3 H32 PAM sing 328 n n 
C4 C5 PAM sing 329 n n 
C4 H41 PAM sing 330 n n 
C4 H42 PAM sing 331 n n 
C5 C6 PAM sing 332 n n 
C5 H51 PAM sing 333 n n 
C5 H52 PAM sing 334 n n 
C6 C7 PAM sing 335 n n 
C6 H61 PAM sing 336 n n 
C6 H62 PAM sing 337 n n 
C7 C8 PAM sing 338 n n 
C7 H71 PAM sing 339 n n 
C7 H72 PAM sing 340 n n 
C8 C9 PAM sing 341 n n 
C8 H81 PAM sing 342 n n 
C8 H82 PAM sing 343 n n 
C9 C10 PAM doub 344 z n 
C9 H9 PAM sing 345 n n 
C10 C11 PAM sing 346 n n 
C10 H10 PAM sing 347 n n 
C11 C12 PAM sing 348 n n 
C11 H111 PAM sing 349 n n 
C11 H112 PAM sing 350 n n 
C12 C13 PAM sing 351 n n 
C12 H121 PAM sing 352 n n 
C12 H122 PAM sing 353 n n 
C13 C14 PAM sing 354 n n 
C13 H131 PAM sing 355 n n 
C13 H132 PAM sing 356 n n 
C14 C15 PAM sing 357 n n 
C14 H141 PAM sing 358 n n 
C14 H142 PAM sing 359 n n 
C15 C16 PAM sing 360 n n 
C15 H151 PAM sing 361 n n 
C15 H152 PAM sing 362 n n 
C16 H161 PAM sing 363 n n 
C16 H162 PAM sing 364 n n 
C16 H163 PAM sing 365 n n 
#
_atom_sites.entry_id                     3EKD 
_atom_sites.fract_transf_matrix[1][1]    0.015682 
_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]    0.007989 
_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]    0.006496 
_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
C 2 PAM A 1 471 465 PAM PAM . 
D 3 HEM A 1 472 462 HEM HEM . 
E 3 HEM B 1 471 463 HEM HEM . 
F 4 HOH A 1 473 1 HOH HOH . 
F 4 HOH A 2 474 2 HOH HOH . 
F 4 HOH A 3 475 3 HOH HOH . 
F 4 HOH A 4 476 4 HOH HOH . 
F 4 HOH A 5 477 5 HOH HOH . 
F 4 HOH A 6 478 7 HOH HOH . 
F 4 HOH A 7 479 8 HOH HOH . 
F 4 HOH A 8 480 9 HOH HOH . 
F 4 HOH A 9 481 11 HOH HOH . 
F 4 HOH A 10 482 13 HOH HOH . 
F 4 HOH A 11 483 14 HOH HOH . 
F 4 HOH A 12 484 17 HOH HOH . 
F 4 HOH A 13 485 19 HOH HOH . 
F 4 HOH A 14 486 21 HOH HOH . 
F 4 HOH A 15 487 22 HOH HOH . 
F 4 HOH A 16 488 23 HOH HOH . 
F 4 HOH A 17 489 26 HOH HOH . 
F 4 HOH A 18 490 27 HOH HOH . 
F 4 HOH A 19 491 29 HOH HOH . 
F 4 HOH A 20 492 30 HOH HOH . 
F 4 HOH A 21 493 31 HOH HOH . 
F 4 HOH A 22 494 32 HOH HOH . 
F 4 HOH A 23 495 33 HOH HOH . 
F 4 HOH A 24 496 34 HOH HOH . 
F 4 HOH A 25 497 39 HOH HOH . 
F 4 HOH A 26 498 40 HOH HOH . 
F 4 HOH A 27 499 41 HOH HOH . 
F 4 HOH A 28 500 42 HOH HOH . 
F 4 HOH A 29 501 44 HOH HOH . 
F 4 HOH A 30 502 45 HOH HOH . 
F 4 HOH A 31 503 46 HOH HOH . 
F 4 HOH A 32 504 48 HOH HOH . 
F 4 HOH A 33 505 49 HOH HOH . 
F 4 HOH A 34 506 54 HOH HOH . 
F 4 HOH A 35 507 59 HOH HOH . 
F 4 HOH A 36 508 61 HOH HOH . 
F 4 HOH A 37 509 62 HOH HOH . 
F 4 HOH A 38 510 63 HOH HOH . 
F 4 HOH A 39 511 64 HOH HOH . 
F 4 HOH A 40 512 65 HOH HOH . 
F 4 HOH A 41 513 66 HOH HOH . 
F 4 HOH A 42 514 69 HOH HOH . 
F 4 HOH A 43 515 71 HOH HOH . 
F 4 HOH A 44 516 73 HOH HOH . 
F 4 HOH A 45 517 74 HOH HOH . 
F 4 HOH A 46 518 75 HOH HOH . 
F 4 HOH A 47 519 81 HOH HOH . 
F 4 HOH A 48 520 85 HOH HOH . 
F 4 HOH A 49 521 86 HOH HOH . 
F 4 HOH A 50 522 88 HOH HOH . 
F 4 HOH A 51 523 89 HOH HOH . 
F 4 HOH A 52 524 90 HOH HOH . 
F 4 HOH A 53 525 91 HOH HOH . 
F 4 HOH A 54 526 92 HOH HOH . 
F 4 HOH A 55 527 93 HOH HOH . 
F 4 HOH A 56 528 94 HOH HOH . 
F 4 HOH A 57 529 95 HOH HOH . 
F 4 HOH A 58 530 97 HOH HOH . 
F 4 HOH A 59 531 98 HOH HOH . 
F 4 HOH A 60 532 99 HOH HOH . 
F 4 HOH A 61 533 100 HOH HOH . 
F 4 HOH A 62 534 101 HOH HOH . 
F 4 HOH A 63 535 105 HOH HOH . 
F 4 HOH A 64 536 106 HOH HOH . 
F 4 HOH A 65 537 107 HOH HOH . 
F 4 HOH A 66 538 108 HOH HOH . 
F 4 HOH A 67 539 109 HOH HOH . 
F 4 HOH A 68 540 110 HOH HOH . 
F 4 HOH A 69 541 111 HOH HOH . 
F 4 HOH A 70 542 113 HOH HOH . 
F 4 HOH A 71 543 116 HOH HOH . 
F 4 HOH A 72 544 117 HOH HOH . 
F 4 HOH A 73 545 119 HOH HOH . 
F 4 HOH A 74 546 120 HOH HOH . 
F 4 HOH A 75 547 122 HOH HOH . 
F 4 HOH A 76 548 124 HOH HOH . 
F 4 HOH A 77 549 125 HOH HOH . 
F 4 HOH A 78 550 126 HOH HOH . 
F 4 HOH A 79 551 128 HOH HOH . 
F 4 HOH A 80 552 129 HOH HOH . 
F 4 HOH A 81 553 131 HOH HOH . 
F 4 HOH A 82 554 132 HOH HOH . 
F 4 HOH A 83 555 133 HOH HOH . 
F 4 HOH A 84 556 135 HOH HOH . 
F 4 HOH A 85 557 136 HOH HOH . 
F 4 HOH A 86 558 138 HOH HOH . 
F 4 HOH A 87 559 139 HOH HOH . 
F 4 HOH A 88 560 140 HOH HOH . 
F 4 HOH A 89 561 142 HOH HOH . 
F 4 HOH A 90 562 143 HOH HOH . 
F 4 HOH A 91 563 144 HOH HOH . 
F 4 HOH A 92 564 145 HOH HOH . 
F 4 HOH A 93 565 146 HOH HOH . 
F 4 HOH A 94 566 147 HOH HOH . 
F 4 HOH A 95 567 148 HOH HOH . 
F 4 HOH A 96 568 150 HOH HOH . 
F 4 HOH A 97 569 152 HOH HOH . 
F 4 HOH A 98 570 153 HOH HOH . 
F 4 HOH A 99 571 154 HOH HOH . 
F 4 HOH A 100 572 160 HOH HOH . 
F 4 HOH A 101 573 162 HOH HOH . 
F 4 HOH A 102 574 165 HOH HOH . 
F 4 HOH A 103 575 166 HOH HOH . 
F 4 HOH A 104 576 167 HOH HOH . 
F 4 HOH A 105 577 168 HOH HOH . 
F 4 HOH A 106 578 169 HOH HOH . 
F 4 HOH A 107 579 170 HOH HOH . 
F 4 HOH A 108 580 171 HOH HOH . 
F 4 HOH A 109 581 173 HOH HOH . 
F 4 HOH A 110 582 175 HOH HOH . 
F 4 HOH A 111 583 176 HOH HOH . 
G 4 HOH B 1 472 6 HOH HOH . 
G 4 HOH B 2 473 10 HOH HOH . 
G 4 HOH B 3 474 12 HOH HOH . 
G 4 HOH B 4 475 15 HOH HOH . 
G 4 HOH B 5 476 16 HOH HOH . 
G 4 HOH B 6 477 18 HOH HOH . 
G 4 HOH B 7 478 20 HOH HOH . 
G 4 HOH B 8 479 25 HOH HOH . 
G 4 HOH B 9 480 28 HOH HOH . 
G 4 HOH B 10 481 35 HOH HOH . 
G 4 HOH B 11 482 36 HOH HOH . 
G 4 HOH B 12 483 38 HOH HOH . 
G 4 HOH B 13 484 43 HOH HOH . 
G 4 HOH B 14 485 47 HOH HOH . 
G 4 HOH B 15 486 50 HOH HOH . 
G 4 HOH B 16 487 51 HOH HOH . 
G 4 HOH B 17 488 52 HOH HOH . 
G 4 HOH B 18 489 53 HOH HOH . 
G 4 HOH B 19 490 55 HOH HOH . 
G 4 HOH B 20 491 56 HOH HOH . 
G 4 HOH B 21 492 57 HOH HOH . 
G 4 HOH B 22 493 58 HOH HOH . 
G 4 HOH B 23 494 60 HOH HOH . 
G 4 HOH B 24 495 67 HOH HOH . 
G 4 HOH B 25 496 68 HOH HOH . 
G 4 HOH B 26 497 70 HOH HOH . 
G 4 HOH B 27 498 72 HOH HOH . 
G 4 HOH B 28 499 76 HOH HOH . 
G 4 HOH B 29 500 77 HOH HOH . 
G 4 HOH B 30 501 78 HOH HOH . 
G 4 HOH B 31 502 79 HOH HOH . 
G 4 HOH B 32 503 80 HOH HOH . 
G 4 HOH B 33 504 82 HOH HOH . 
G 4 HOH B 34 505 83 HOH HOH . 
G 4 HOH B 35 506 84 HOH HOH . 
G 4 HOH B 36 507 87 HOH HOH . 
G 4 HOH B 37 508 96 HOH HOH . 
G 4 HOH B 38 509 102 HOH HOH . 
G 4 HOH B 39 510 103 HOH HOH . 
G 4 HOH B 40 511 104 HOH HOH . 
G 4 HOH B 41 512 112 HOH HOH . 
G 4 HOH B 42 513 114 HOH HOH . 
G 4 HOH B 43 514 115 HOH HOH . 
G 4 HOH B 44 515 118 HOH HOH . 
G 4 HOH B 45 516 121 HOH HOH . 
G 4 HOH B 46 517 123 HOH HOH . 
G 4 HOH B 47 518 127 HOH HOH . 
G 4 HOH B 48 519 130 HOH HOH . 
G 4 HOH B 49 520 134 HOH HOH . 
G 4 HOH B 50 521 141 HOH HOH . 
G 4 HOH B 51 522 149 HOH HOH . 
G 4 HOH B 52 523 151 HOH HOH . 
G 4 HOH B 53 524 155 HOH HOH . 
G 4 HOH B 54 525 156 HOH HOH . 
G 4 HOH B 55 526 157 HOH HOH . 
G 4 HOH B 56 527 158 HOH HOH . 
G 4 HOH B 57 528 159 HOH HOH . 
G 4 HOH B 58 529 161 HOH HOH . 
G 4 HOH B 59 530 164 HOH HOH . 
G 4 HOH B 60 531 172 HOH HOH . 
G 4 HOH B 61 532 174 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 PAM . . . C 2 4.664 55.033 5.989 1 60.26 ? C1 PAM 471 A 1 
HETATM 2 O O1 PAM . . . C 2 5.149 54.194 5.178 1 61.72 ? O1 PAM 471 A 1 
HETATM 3 O O2 PAM . . . C 2 4.45 56.24 5.599 1 57.4 ? O2 PAM 471 A 1 
HETATM 4 C C2 PAM . . . C 2 4.371 54.574 7.431 1 58.95 ? C2 PAM 471 A 1 
HETATM 5 C C3 PAM . . . C 2 4.488 53.061 7.776 1 56.97 ? C3 PAM 471 A 1 
HETATM 6 C C4 PAM . . . C 2 5.884 52.554 8.191 1 54.7 ? C4 PAM 471 A 1 
HETATM 7 C C5 PAM . . . C 2 5.867 51.13 8.78 1 52.95 ? C5 PAM 471 A 1 
HETATM 8 C C6 PAM . . . C 2 7.101 50.834 9.647 1 52.75 ? C6 PAM 471 A 1 
HETATM 9 C C7 PAM . . . C 2 7.164 49.447 10.32 1 51.38 ? C7 PAM 471 A 1 
HETATM 10 C C8 PAM . . . C 2 8.365 49.354 11.297 1 50.87 ? C8 PAM 471 A 1 
HETATM 11 C C9 PAM . . . C 2 8.312 48.113 12.219 1 48.82 ? C9 PAM 471 A 1 
HETATM 12 C C10 PAM . . . C 2 9.246 48.145 13.436 1 47.61 ? C10 PAM 471 A 1 
HETATM 13 C C11 PAM . . . C 2 9.297 49.495 14.148 1 47.04 ? C11 PAM 471 A 1 
HETATM 14 C C12 PAM . . . C 2 9.647 49.425 15.638 1 48.19 ? C12 PAM 471 A 1 
HETATM 15 C C13 PAM . . . C 2 11.144 49.279 15.936 1 48.51 ? C13 PAM 471 A 1 
HETATM 16 C C14 PAM . . . C 2 11.512 49.448 17.423 1 49.13 ? C14 PAM 471 A 1 
HETATM 17 C C15 PAM . . . C 2 12.834 50.19 17.739 1 50.37 ? C15 PAM 471 A 1 
HETATM 18 C C16 PAM . . . C 2 13.987 49.343 18.315 1 48.96 ? C16 PAM 471 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           18 
#