data_8UE9 # _model_server_result.job_id jznuHKfkynSAqGhbTsbDPw _model_server_result.datetime_utc '2024-11-22 19:13:53' _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 8ue9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":604}' # _entry.id 8UE9 # _exptl.entry_id 8UE9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 537.901 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE _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 8UE9 _cell.length_a 67.069 _cell.length_b 119.776 _cell.length_c 129.708 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UE9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,Y _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _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 59 A CYS 93 1_555 B SG CYS 59 B CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A SG CYS 97 A CYS 131 1_555 E C17 WUU . A WUU 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? covale ? covale2 B SG CYS 97 B CYS 131 1_555 U C17 WUU . B WUU 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? metalc ? metalc1 A O THR 108 A THR 142 1_555 G K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.221 ? metalc ? metalc2 A OG1 THR 108 A THR 142 1_555 G K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? metalc ? metalc3 A O THR 108 A THR 142 1_555 J K K . A K 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc4 A O GLY 110 A GLY 144 1_555 H K K . A K 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? metalc ? metalc5 A O GLY 110 A GLY 144 1_555 I K K . A K 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc6 A O PHE 111 A PHE 145 1_555 H K K . A K 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc7 A O THR 217 A THR 251 1_555 G K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? metalc ? metalc8 A OG1 THR 217 A THR 251 1_555 G K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc9 A O THR 217 A THR 251 1_555 J K K . A K 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc10 A O ILE 218 A ILE 252 1_555 I K K . A K 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc11 A O ILE 218 A ILE 252 1_555 J K K . A K 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? metalc ? metalc12 A O GLY 219 A GLY 253 1_555 H K K . A K 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc13 A O GLY 219 A GLY 253 1_555 I K K . A K 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc14 A O PHE 220 A PHE 254 1_555 H K K . A K 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? metalc ? metalc15 G K K . A K 605 1_555 B O THR 108 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.26 ? metalc ? metalc16 G K K . A K 605 1_555 B OG1 THR 108 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc17 G K K . A K 605 1_555 B O THR 217 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? metalc ? metalc18 G K K . A K 605 1_555 B OG1 THR 217 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? metalc ? metalc19 H K K . A K 606 1_555 B O GLY 110 B GLY 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc20 H K K . A K 606 1_555 B O PHE 111 B PHE 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc21 H K K . A K 606 1_555 B O GLY 219 B GLY 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? metalc ? metalc22 H K K . A K 606 1_555 B O PHE 220 B PHE 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc23 I K K . A K 607 1_555 B O GLY 110 B GLY 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc24 I K K . A K 607 1_555 B O ILE 218 B ILE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc25 I K K . A K 607 1_555 B O GLY 219 B GLY 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc26 J K K . A K 608 1_555 B O THR 108 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc27 J K K . A K 608 1_555 B O THR 217 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc28 J K K . A K 608 1_555 B O ILE 218 B ILE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? # _chem_comp.formula 'C34 H67 N O3' _chem_comp.formula_weight 537.901 _chem_comp.id 16C _chem_comp.mon_nstd_flag . _chem_comp.name N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms C16-CERAMIDE;N-PALMITOYL-D-ERYTHRO-SPHINGOSINE;(2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL;(2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL # 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 O19 C19 16C doub 1 n n C19 N2 16C sing 2 n n C19 C20 16C sing 3 n n N2 C2 16C sing 4 n n N2 HN2 16C sing 5 n n C2 C1 16C sing 6 n n C2 C3 16C sing 7 n n C2 H2 16C sing 8 n n C1 O1 16C sing 9 n n C1 H11 16C sing 10 n n C1 H12 16C sing 11 n n O1 HO1 16C sing 12 n n C3 C4 16C sing 13 n n C3 O3 16C sing 14 n n C3 H3 16C sing 15 n n C4 C5 16C doub 16 e n C4 H4 16C sing 17 n n C5 C6 16C sing 18 n n C5 H5 16C sing 19 n n C6 C7 16C sing 20 n n C6 H61 16C sing 21 n n C6 H62 16C sing 22 n n C7 C8 16C sing 23 n n C7 H71 16C sing 24 n n C7 H72 16C sing 25 n n C8 C9 16C sing 26 n n C8 H81 16C sing 27 n n C8 H82 16C sing 28 n n C9 C10 16C sing 29 n n C9 H91 16C sing 30 n n C9 H92 16C sing 31 n n C10 C11 16C sing 32 n n C10 H101 16C sing 33 n n C10 H102 16C sing 34 n n C11 C12 16C sing 35 n n C11 H111 16C sing 36 n n C11 H112 16C sing 37 n n C12 C13 16C sing 38 n n C12 H121 16C sing 39 n n C12 H122 16C sing 40 n n C13 C14 16C sing 41 n n C13 H131 16C sing 42 n n C13 H132 16C sing 43 n n C14 C15 16C sing 44 n n C14 H141 16C sing 45 n n C14 H142 16C sing 46 n n C15 C16 16C sing 47 n n C15 H151 16C sing 48 n n C15 H152 16C sing 49 n n C16 C17 16C sing 50 n n C16 H161 16C sing 51 n n C16 H162 16C sing 52 n n C17 C18 16C sing 53 n n C17 H171 16C sing 54 n n C17 H172 16C sing 55 n n C18 H181 16C sing 56 n n C18 H182 16C sing 57 n n C18 H183 16C sing 58 n n O3 HO3 16C sing 59 n n C20 C21 16C sing 60 n n C20 H201 16C sing 61 n n C20 H202 16C sing 62 n n C21 C22 16C sing 63 n n C21 H211 16C sing 64 n n C21 H212 16C sing 65 n n C22 C23 16C sing 66 n n C22 H221 16C sing 67 n n C22 H222 16C sing 68 n n C23 C24 16C sing 69 n n C23 H231 16C sing 70 n n C23 H232 16C sing 71 n n C24 C25 16C sing 72 n n C24 H241 16C sing 73 n n C24 H242 16C sing 74 n n C25 C26 16C sing 75 n n C25 H251 16C sing 76 n n C25 H252 16C sing 77 n n C26 C27 16C sing 78 n n C26 H261 16C sing 79 n n C26 H262 16C sing 80 n n C27 C28 16C sing 81 n n C27 H271 16C sing 82 n n C27 H272 16C sing 83 n n C28 C29 16C sing 84 n n C28 H281 16C sing 85 n n C28 H282 16C sing 86 n n C29 C30 16C sing 87 n n C29 H291 16C sing 88 n n C29 H292 16C sing 89 n n C30 C31 16C sing 90 n n C30 H301 16C sing 91 n n C30 H302 16C sing 92 n n C31 C32 16C sing 93 n n C31 H311 16C sing 94 n n C31 H312 16C sing 95 n n C32 C33 16C sing 96 n n C32 H321 16C sing 97 n n C32 H322 16C sing 98 n n C33 C34 16C sing 99 n n C33 H331 16C sing 100 n n C33 H332 16C sing 101 n n C34 H341 16C sing 102 n n C34 H342 16C sing 103 n n C34 H343 16C sing 104 n n # _atom_sites.entry_id 8UE9 _atom_sites.fract_transf_matrix[1][1] 0.01491 _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] 0.008349 _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] 0.00771 _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 R16 A 1 601 601 R16 R16 . D 2 R16 A 1 602 701 R16 R16 . E 3 WUU A 1 603 1001 WUU MLA . F 4 16C A 1 604 701 16C 16C . G 5 K A 1 605 1 K K . H 5 K A 1 606 3 K K . I 5 K A 1 607 4 K K . J 5 K A 1 608 6 K K . K 5 K A 1 609 7 K K . L 2 R16 A 1 610 15 R16 R16 . M 2 R16 A 1 611 16 R16 R16 . N 2 R16 A 1 612 18 R16 R16 . O 2 R16 A 1 613 19 R16 R16 . P 2 R16 A 1 614 20 R16 R16 . Q 2 R16 A 1 615 21 R16 R16 . R 2 R16 B 1 401 401 R16 R16 . S 2 R16 B 1 402 501 R16 R16 . T 2 R16 B 1 403 601 R16 R16 . U 3 WUU B 1 404 801 WUU MLA . V 2 R16 B 1 405 2 R16 R16 . W 2 R16 B 1 406 17 R16 R16 . X 6 CD B 1 407 1 CD CD . Y 7 HOH B 1 501 1 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 O O19 16C . . . F 4 7.877 -39.846 -48.445 1 204.21 ? O19 16C 604 A 1 HETATM 2 C C19 16C . . . F 4 6.889 -39.477 -48.982 1 206.43 ? C19 16C 604 A 1 HETATM 3 N N2 16C . . . F 4 5.589 -39.842 -48.37 1 210.66 ? N2 16C 604 A 1 HETATM 4 C C2 16C . . . F 4 4.222 -39.503 -48.844 1 229.26 ? C2 16C 604 A 1 HETATM 5 C C1 16C . . . F 4 3.989 -38.001 -48.864 1 223.52 ? C1 16C 604 A 1 HETATM 6 O O1 16C . . . F 4 3.466 -37.618 -47.627 1 216.47 ? O1 16C 604 A 1 HETATM 7 C C3 16C . . . F 4 3.881 -40.154 -50.194 1 224.66 ? C3 16C 604 A 1 HETATM 8 C C4 16C . . . F 4 3.745 -39.089 -51.31 1 216.54 ? C4 16C 604 A 1 HETATM 9 C C5 16C . . . F 4 4.016 -39.417 -52.587 1 214.08 ? C5 16C 604 A 1 HETATM 10 C C6 16C . . . F 4 3.89 -38.37 -53.726 1 204.99 ? C6 16C 604 A 1 HETATM 11 C C7 16C . . . F 4 2.914 -37.194 -53.388 1 191.83 ? C7 16C 604 A 1 HETATM 12 C C8 16C . . . F 4 3.655 -35.936 -52.848 1 201.75 ? C8 16C 604 A 1 HETATM 13 C C9 16C . . . F 4 3.048 -35.426 -51.528 1 199.82 ? C9 16C 604 A 1 HETATM 14 C C10 16C . . . F 4 1.508 -35.256 -51.619 1 198.27 ? C10 16C 604 A 1 HETATM 15 C C11 16C . . . F 4 0.758 -36.073 -50.54 1 202.25 ? C11 16C 604 A 1 HETATM 16 C C12 16C . . . F 4 -0.035 -37.261 -51.161 1 212.96 ? C12 16C 604 A 1 HETATM 17 C C13 16C . . . F 4 -1.419 -36.822 -51.723 1 212.65 ? C13 16C 604 A 1 HETATM 18 C C14 16C . . . F 4 -2.547 -36.986 -50.695 1 204.32 ? C14 16C 604 A 1 HETATM 19 C C15 16C . . . F 4 -3.283 -35.674 -50.399 1 180.88 ? C15 16C 604 A 1 HETATM 20 C C16 16C . . . F 4 -3.231 -34.672 -51.584 1 166.36 ? C16 16C 604 A 1 HETATM 21 C C17 16C . . . F 4 -2.882 -33.242 -51.12 1 168.22 ? C17 16C 604 A 1 HETATM 22 C C18 16C . . . F 4 -1.375 -32.964 -51.175 1 166.38 ? C18 16C 604 A 1 HETATM 23 O O3 16C . . . F 4 4.862 -41.075 -50.546 1 220.43 ? O3 16C 604 A 1 HETATM 24 C C20 16C . . . F 4 7.036 -38.643 -50.291 1 213.76 ? C20 16C 604 A 1 HETATM 25 C C21 16C . . . F 4 8.308 -39.029 -51.093 1 220.2 ? C21 16C 604 A 1 HETATM 26 C C22 16C . . . F 4 9.254 -37.803 -51.346 1 207.92 ? C22 16C 604 A 1 HETATM 27 C C23 16C . . . F 4 10.427 -37.741 -50.321 1 196.5 ? C23 16C 604 A 1 HETATM 28 C C24 16C . . . F 4 10.84 -36.277 -49.989 1 189.94 ? C24 16C 604 A 1 HETATM 29 C C25 16C . . . F 4 10.591 -35.92 -48.471 1 190.03 ? C25 16C 604 A 1 HETATM 30 C C26 16C . . . F 4 9.164 -36.338 -47.992 1 195.61 ? C26 16C 604 A 1 HETATM 31 C C27 16C . . . F 4 8.296 -35.1 -47.595 1 188.66 ? C27 16C 604 A 1 HETATM 32 C C28 16C . . . F 4 6.771 -35.288 -47.934 1 177.02 ? C28 16C 604 A 1 HETATM 33 C C29 16C . . . F 4 6.386 -34.622 -49.299 1 170.74 ? C29 16C 604 A 1 HETATM 34 C C30 16C . . . F 4 6.931 -33.171 -49.429 1 165.87 ? C30 16C 604 A 1 HETATM 35 C C31 16C . . . F 4 6.349 -32.204 -48.352 1 155.98 ? C31 16C 604 A 1 HETATM 36 C C32 16C . . . F 4 6.498 -30.715 -48.751 1 148.95 ? C32 16C 604 A 1 HETATM 37 C C33 16C . . . F 4 6.706 -29.794 -47.526 1 144.92 ? C33 16C 604 A 1 HETATM 38 C C34 16C . . . F 4 7.192 -28.39 -47.923 1 145.24 ? C34 16C 604 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 38 #