data_5NDC
#
_model_server_result.job_id            tUyt34lo-u2cWi6snSZUDw 
_model_server_result.datetime_utc      '2025-03-01 00:52:23' 
_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          5ndc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":202}' 
#
_entry.id    5NDC 
#
_exptl.entry_id    5NDC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              356.54 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' 
_entity.pdbx_number_of_molecules    15 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          126.76 
_cell.angle_gamma         90 
_cell.entry_id            5NDC 
_cell.length_a            145.85 
_cell.length_b            100.32 
_cell.length_c            96.62 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NDC 
_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    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,V,W,X 
_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    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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 7 G N N 
? 7 H N N 
? 7 I N N 
? 7 J N N 
? 7 K N N 
? 7 L N N 
? 7 M N N 
? 7 N N N 
? 7 O N N 
? 7 P N N 
? 7 Q N N 
? 7 S N N 
? 7 T N N 
? 7 U N N 
? 7 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
metalc ? metalc1 A NE2 HIS 79 A HIS 72 1_555 E FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc2 A ND1 HIS 240 A HIS 233 1_555 D CU CU . A CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? 
metalc ? metalc3 A NE2 HIS 289 A HIS 282 1_555 D CU CU . A CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc4 A NE2 HIS 290 A HIS 283 1_555 D CU CU . A CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? 
metalc ? metalc5 A NE2 HIS 391 A HIS 384 1_555 F FE HAS . A HAS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc6 A NE2 HIS 393 A HIS 386 1_555 E FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc7 D CU CU . A CU 601 1_555 W O HOH . A HOH 752 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc8 B ND1 HIS 114 B HIS 114 1_555 R CU2 CUA . B CUA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc9 B SG CYS 149 B CYS 149 1_555 R CU1 CUA . B CUA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc10 B SG CYS 149 B CYS 149 1_555 R CU2 CUA . B CUA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc11 B O GLN 151 B GLN 151 1_555 R CU1 CUA . B CUA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? 
metalc ? metalc12 B SG CYS 153 B CYS 153 1_555 R CU1 CUA . B CUA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc13 B SG CYS 153 B CYS 153 1_555 R CU2 CUA . B CUA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc14 B ND1 HIS 157 B HIS 157 1_555 R CU1 CUA . B CUA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
metalc ? metalc15 B SD MET 160 B MET 160 1_555 R CU2 CUA . B CUA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
#
_chem_comp.formula           'C21 H40 O4' 
_chem_comp.formula_weight    356.54 
_chem_comp.id                OLC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1-Oleoyl-R-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
C18 C17 OLC sing 456 n n 
C10 C9 OLC doub 457 n n 
C10 C11 OLC sing 458 n n 
C9 C8 OLC sing 459 n n 
C17 C16 OLC sing 460 z n 
C11 C12 OLC sing 461 n n 
C8 C7 OLC sing 462 n n 
C24 C22 OLC sing 463 n n 
C24 O25 OLC sing 464 n n 
C16 C15 OLC sing 465 n n 
C12 C13 OLC sing 466 n n 
C7 C6 OLC sing 467 n n 
C15 C14 OLC sing 468 n n 
C13 C14 OLC sing 469 n n 
C6 C5 OLC sing 470 n n 
C5 C4 OLC sing 471 n n 
C4 C3 OLC sing 472 n n 
C3 C2 OLC sing 473 n n 
C2 C1 OLC sing 474 n n 
C21 C22 OLC sing 475 n n 
C21 O20 OLC sing 476 n n 
C1 O19 OLC doub 477 n n 
C1 O20 OLC sing 478 n n 
C22 O23 OLC sing 479 n n 
C18 H18 OLC sing 480 n n 
C18 H18A OLC sing 481 n n 
C18 H18B OLC sing 482 n n 
C10 H10 OLC sing 483 n n 
C9 H9 OLC sing 484 n n 
C17 H17 OLC sing 485 n n 
C17 H17A OLC sing 486 n n 
C11 H11 OLC sing 487 n n 
C11 H11A OLC sing 488 n n 
C8 H8 OLC sing 489 n n 
C8 H8A OLC sing 490 n n 
C24 H24 OLC sing 491 n n 
C24 H24A OLC sing 492 n n 
C16 H16 OLC sing 493 n n 
C16 H16A OLC sing 494 n n 
C12 H12 OLC sing 495 n n 
C12 H12A OLC sing 496 n n 
C7 H7 OLC sing 497 n n 
C7 H7A OLC sing 498 n n 
C15 H15 OLC sing 499 n n 
C15 H15A OLC sing 500 n n 
C13 H13 OLC sing 501 n n 
C13 H13A OLC sing 502 n n 
C6 H6 OLC sing 503 n n 
C6 H6A OLC sing 504 n n 
C14 H14 OLC sing 505 n n 
C14 H14A OLC sing 506 n n 
C5 H5 OLC sing 507 n n 
C5 H5A OLC sing 508 n n 
C4 H4 OLC sing 509 n n 
C4 H4A OLC sing 510 n n 
C3 H3 OLC sing 511 n n 
C3 H3A OLC sing 512 n n 
C2 H2 OLC sing 513 n n 
C2 H2A OLC sing 514 n n 
C21 H21 OLC sing 515 n n 
C21 H21A OLC sing 516 n n 
C22 H22 OLC sing 517 n n 
O25 HO25 OLC sing 518 n n 
O23 HO23 OLC sing 519 n n 
#
_atom_sites.entry_id                     5NDC 
_atom_sites.fract_transf_matrix[1][1]    0.006856 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005122 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009968 
_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]    0.012919 
_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
D 4 CU A 1 601 803 CU CU . 
E 5 HEM A 1 602 800 HEM HEM . 
F 6 HAS A 1 603 801 HAS HAS . 
G 7 OLC A 1 604 566 OLC OLC . 
H 7 OLC A 1 605 567 OLC OLC . 
I 7 OLC A 1 606 568 OLC OLC . 
J 7 OLC A 1 607 570 OLC OLC . 
K 7 OLC A 1 608 571 OLC OLC . 
L 7 OLC A 1 609 572 OLC OLC . 
M 7 OLC A 1 610 573 OLC OLC . 
N 7 OLC A 1 611 574 OLC OLC . 
O 7 OLC A 1 612 172 OLC OLC . 
P 7 OLC A 1 613 564 OLC OLC . 
Q 7 OLC A 1 614 565 OLC OLC . 
R 8 CUA B 1 201 802 CUA CUA . 
S 7 OLC B 1 202 169 OLC OLC . 
T 7 OLC C 1 101 564 OLC OLC . 
U 7 OLC C 1 102 170 OLC OLC . 
V 7 OLC C 1 103 171 OLC OLC . 
W 9 HOH A 1 701 108 HOH HOH . 
W 9 HOH A 2 702 122 HOH HOH . 
W 9 HOH A 3 703 119 HOH HOH . 
W 9 HOH A 4 704 96 HOH HOH . 
W 9 HOH A 5 705 76 HOH HOH . 
W 9 HOH A 6 706 109 HOH HOH . 
W 9 HOH A 7 707 38 HOH HOH . 
W 9 HOH A 8 708 20 HOH HOH . 
W 9 HOH A 9 709 32 HOH HOH . 
W 9 HOH A 10 710 37 HOH HOH . 
W 9 HOH A 11 711 11 HOH HOH . 
W 9 HOH A 12 712 8 HOH HOH . 
W 9 HOH A 13 713 84 HOH HOH . 
W 9 HOH A 14 714 23 HOH HOH . 
W 9 HOH A 15 715 60 HOH HOH . 
W 9 HOH A 16 716 45 HOH HOH . 
W 9 HOH A 17 717 3 HOH HOH . 
W 9 HOH A 18 718 90 HOH HOH . 
W 9 HOH A 19 719 16 HOH HOH . 
W 9 HOH A 20 720 35 HOH HOH . 
W 9 HOH A 21 721 17 HOH HOH . 
W 9 HOH A 22 722 25 HOH HOH . 
W 9 HOH A 23 723 33 HOH HOH . 
W 9 HOH A 24 724 4 HOH HOH . 
W 9 HOH A 25 725 81 HOH HOH . 
W 9 HOH A 26 726 2 HOH HOH . 
W 9 HOH A 27 727 19 HOH HOH . 
W 9 HOH A 28 728 87 HOH HOH . 
W 9 HOH A 29 729 36 HOH HOH . 
W 9 HOH A 30 730 47 HOH HOH . 
W 9 HOH A 31 731 10 HOH HOH . 
W 9 HOH A 32 732 26 HOH HOH . 
W 9 HOH A 33 733 44 HOH HOH . 
W 9 HOH A 34 734 12 HOH HOH . 
W 9 HOH A 35 735 55 HOH HOH . 
W 9 HOH A 36 736 24 HOH HOH . 
W 9 HOH A 37 737 46 HOH HOH . 
W 9 HOH A 38 738 1 HOH HOH . 
W 9 HOH A 39 739 41 HOH HOH . 
W 9 HOH A 40 740 27 HOH HOH . 
W 9 HOH A 41 741 15 HOH HOH . 
W 9 HOH A 42 742 92 HOH HOH . 
W 9 HOH A 43 743 40 HOH HOH . 
W 9 HOH A 44 744 31 HOH HOH . 
W 9 HOH A 45 745 51 HOH HOH . 
W 9 HOH A 46 746 94 HOH HOH . 
W 9 HOH A 47 747 56 HOH HOH . 
W 9 HOH A 48 748 5 HOH HOH . 
W 9 HOH A 49 749 22 HOH HOH . 
W 9 HOH A 50 750 67 HOH HOH . 
W 9 HOH A 51 751 120 HOH HOH . 
W 9 HOH A 52 752 123 HOH HOH . 
W 9 HOH A 53 753 72 HOH HOH . 
W 9 HOH A 54 754 57 HOH HOH . 
W 9 HOH A 55 755 95 HOH HOH . 
W 9 HOH A 56 756 98 HOH HOH . 
W 9 HOH A 57 757 111 HOH HOH . 
W 9 HOH A 58 758 48 HOH HOH . 
X 9 HOH B 1 301 59 HOH HOH . 
X 9 HOH B 2 302 50 HOH HOH . 
X 9 HOH B 3 303 86 HOH HOH . 
X 9 HOH B 4 304 117 HOH HOH . 
X 9 HOH B 5 305 54 HOH HOH . 
X 9 HOH B 6 306 34 HOH HOH . 
X 9 HOH B 7 307 29 HOH HOH . 
X 9 HOH B 8 308 7 HOH HOH . 
X 9 HOH B 9 309 61 HOH HOH . 
X 9 HOH B 10 310 43 HOH HOH . 
X 9 HOH B 11 311 64 HOH HOH . 
X 9 HOH B 12 312 39 HOH HOH . 
X 9 HOH B 13 313 79 HOH HOH . 
X 9 HOH B 14 314 28 HOH HOH . 
X 9 HOH B 15 315 13 HOH HOH . 
X 9 HOH B 16 316 70 HOH HOH . 
X 9 HOH B 17 317 18 HOH HOH . 
X 9 HOH B 18 318 53 HOH HOH . 
X 9 HOH B 19 319 66 HOH HOH . 
X 9 HOH B 20 320 30 HOH HOH . 
X 9 HOH B 21 321 71 HOH HOH . 
X 9 HOH B 22 322 14 HOH HOH . 
X 9 HOH B 23 323 65 HOH HOH . 
X 9 HOH B 24 324 49 HOH HOH . 
X 9 HOH B 25 325 73 HOH HOH . 
X 9 HOH B 26 326 69 HOH HOH . 
X 9 HOH B 27 327 21 HOH HOH . 
X 9 HOH B 28 328 9 HOH HOH . 
X 9 HOH B 29 329 83 HOH HOH . 
X 9 HOH B 30 330 6 HOH HOH . 
X 9 HOH B 31 331 42 HOH HOH . 
X 9 HOH B 32 332 97 HOH HOH . 
X 9 HOH B 33 333 85 HOH HOH . 
X 9 HOH B 34 334 75 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 C18 OLC . . . S 7 2.657 -13.855 -4.616 1 67.7 ? C18 OLC 202 B 1 
HETATM 2 C C10 OLC . . . S 7 -4.379 -11.535 0.815 1 69.95 ? C10 OLC 202 B 1 
HETATM 3 C C9 OLC . . . S 7 -5.62 -11.406 1.338 1 68.36 ? C9 OLC 202 B 1 
HETATM 4 C C17 OLC . . . S 7 1.138 -13.895 -4.615 1 67.65 ? C17 OLC 202 B 1 
HETATM 5 C C11 OLC . . . S 7 -4.123 -11.568 -0.684 1 69.51 ? C11 OLC 202 B 1 
HETATM 6 C C8 OLC . . . S 7 -6.869 -11.318 0.477 1 68.19 ? C8 OLC 202 B 1 
HETATM 7 C C24 OLC . . . S 7 -17.25 -11.881 6.13 1 90.05 ? C24 OLC 202 B 1 
HETATM 8 C C16 OLC . . . S 7 0.511 -12.534 -4.968 1 67.93 ? C16 OLC 202 B 1 
HETATM 9 C C12 OLC . . . S 7 -2.66 -11.782 -1.078 1 67.78 ? C12 OLC 202 B 1 
HETATM 10 C C7 OLC . . . S 7 -8.013 -10.511 1.089 1 69.32 ? C7 OLC 202 B 1 
HETATM 11 C C15 OLC . . . S 7 -0.971 -12.399 -4.558 1 67.11 ? C15 OLC 202 B 1 
HETATM 12 C C13 OLC . . . S 7 -2.503 -11.746 -2.607 1 66.28 ? C13 OLC 202 B 1 
HETATM 13 C C6 OLC . . . S 7 -9.299 -11.331 1.271 1 70.79 ? C6 OLC 202 B 1 
HETATM 14 C C14 OLC . . . S 7 -1.145 -12.286 -3.039 1 66.51 ? C14 OLC 202 B 1 
HETATM 15 C C5 OLC . . . S 7 -10.545 -10.444 1.36 1 71.55 ? C5 OLC 202 B 1 
HETATM 16 C C4 OLC . . . S 7 -11.814 -11.257 1.631 1 72.48 ? C4 OLC 202 B 1 
HETATM 17 C C3 OLC . . . S 7 -12.059 -11.461 3.134 1 74.31 ? C3 OLC 202 B 1 
HETATM 18 C C2 OLC . . . S 7 -13.363 -12.237 3.397 1 76.82 ? C2 OLC 202 B 1 
HETATM 19 C C21 OLC . . . S 7 -15.145 -13.187 6.724 1 85.98 ? C21 OLC 202 B 1 
HETATM 20 C C1 OLC . . . S 7 -13.521 -12.716 4.833 1 78.09 ? C1 OLC 202 B 1 
HETATM 21 C C22 OLC . . . S 7 -16.642 -12.98 7.002 1 89.07 ? C22 OLC 202 B 1 
HETATM 22 O O19 OLC . . . S 7 -12.572 -12.698 5.597 1 79.01 ? O19 OLC 202 B 1 
HETATM 23 O O25 OLC . . . S 7 -18.237 -11.147 6.867 1 90.45 ? O25 OLC 202 B 1 
HETATM 24 O O23 OLC . . . S 7 -17.372 -14.188 6.783 1 93.95 ? O23 OLC 202 B 1 
HETATM 25 O O20 OLC . . . S 7 -14.814 -13.211 5.324 1 82.21 ? O20 OLC 202 B 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           69 
_model_server_stats.create_model_time_ms    75 
_model_server_stats.query_time_ms           1421 
_model_server_stats.encode_time_ms          19 
_model_server_stats.element_count           25 
#