data_8UF6 # _model_server_result.job_id 5Ko-P1M7ghIXYyC-n2l0Ig _model_server_result.datetime_utc '2024-11-14 16:57:35' _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 8uf6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":409}' # _entry.id 8UF6 # _exptl.entry_id 8UF6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 537.901 _entity.id 5 _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 2 _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 8UF6 _cell.length_a 66.953 _cell.length_b 118.597 _cell.length_c 130.873 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UF6 _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 _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 ? 5 I N N ? 5 R 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 disulf ? disulf1 A SG CYS 59 A CYS 93 1_555 B SG CYS 59 B CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A OG SER 97 A SER 131 1_555 C C23 WRZ . A WRZ 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale2 B OG SER 97 B SER 131 1_555 J C23 WRZ . B WRZ 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? metalc ? metalc1 A O THR 108 A THR 142 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.042 ? metalc ? metalc2 A OG1 THR 108 A THR 142 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.067 ? metalc ? metalc3 A O THR 108 A THR 142 1_555 N K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc4 A O ILE 109 A ILE 143 1_555 G K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc5 A O ILE 109 A ILE 143 1_555 N K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc6 A O GLY 110 A GLY 144 1_555 G K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc7 A O GLY 110 A GLY 144 1_555 M K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc8 A O PHE 111 A PHE 145 1_555 M K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc9 A O THR 217 A THR 251 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc10 A OG1 THR 217 A THR 251 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc11 A O THR 217 A THR 251 1_555 N K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc12 A O ILE 218 A ILE 252 1_555 G K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc13 A O ILE 218 A ILE 252 1_555 N K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? metalc ? metalc14 A O GLY 219 A GLY 253 1_555 G K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc15 A O GLY 219 A GLY 253 1_555 M K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.093 ? metalc ? metalc16 A O PHE 220 A PHE 254 1_555 M K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc17 G K K . A K 405 1_555 B O ILE 109 B ILE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc18 G K K . A K 405 1_555 B O GLY 110 B GLY 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc19 G K K . A K 405 1_555 B O ILE 218 B ILE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc20 G K K . A K 405 1_555 B O GLY 219 B GLY 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc21 H K K . A K 406 1_555 B O THR 108 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc22 H K K . A K 406 1_555 B OG1 THR 108 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc23 H K K . A K 406 1_555 B O THR 217 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc24 H K K . A K 406 1_555 B OG1 THR 217 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc25 B O THR 108 B THR 142 1_555 N K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? metalc ? metalc26 B O ILE 109 B ILE 143 1_555 N K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? metalc ? metalc27 B O GLY 110 B GLY 144 1_555 M K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.004 ? metalc ? metalc28 B O PHE 111 B PHE 145 1_555 M K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc29 B O THR 217 B THR 251 1_555 N K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc30 B O ILE 218 B ILE 252 1_555 N K K . B K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc31 B O GLY 219 B GLY 253 1_555 M K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.016 ? metalc ? metalc32 B O PHE 220 B PHE 254 1_555 M K K . B K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc33 B OE1 GLU 275 B GLU 309 1_555 P CD CD . B CD 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? # _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 8UF6 _atom_sites.fract_transf_matrix[1][1] 0.014936 _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] 0.008432 _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] 0.007641 _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 WRZ A 1 401 3 WRZ LH9 . D 3 D10 A 1 402 1 D10 D10 . E 3 D10 A 1 403 2 D10 D10 . F 4 K A 1 404 2 K K . G 4 K A 1 405 4 K K . H 4 K A 1 406 6 K K . I 5 16C A 1 407 1 16C 16C . J 2 WRZ B 1 401 4 WRZ LH9 . K 6 1PE B 1 402 1 1PE 1PE . L 4 K B 1 403 1 K K . M 4 K B 1 404 3 K K . N 4 K B 1 405 5 K K . O 7 CD B 1 406 1 CD CD . P 7 CD B 1 407 2 CD CD . Q 8 D12 B 1 408 1 D12 D12 . R 5 16C B 1 409 2 16C 16C . S 9 OCT B 1 410 1 OCT OCT . T 9 OCT B 1 411 2 OCT OCT . U 10 R16 B 1 412 1 R16 R16 . # 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 . . . R 5 -6.704 -33.422 46.21 1 121 ? O19 16C 409 B 1 HETATM 2 C C19 16C . . . R 5 -6.561 -33.339 47.374 1 119.09 ? C19 16C 409 B 1 HETATM 3 N N2 16C . . . R 5 -6.803 -34.517 48.235 1 121.16 ? N2 16C 409 B 1 HETATM 4 C C2 16C . . . R 5 -7.226 -35.786 47.637 1 141.05 ? C2 16C 409 B 1 HETATM 5 C C1 16C . . . R 5 -6.115 -36.813 47.753 1 132.11 ? C1 16C 409 B 1 HETATM 6 O O1 16C . . . R 5 -6.432 -37.93 46.973 1 129.35 ? O1 16C 409 B 1 HETATM 7 C C3 16C . . . R 5 -8.474 -36.299 48.359 1 145.01 ? C3 16C 409 B 1 HETATM 8 C C4 16C . . . R 5 -9.591 -35.219 48.283 1 144.5 ? C4 16C 409 B 1 HETATM 9 C C5 16C . . . R 5 -10.904 -35.559 48.349 1 126.12 ? C5 16C 409 B 1 HETATM 10 C C6 16C . . . R 5 -11.99 -34.447 48.27 1 120.15 ? C6 16C 409 B 1 HETATM 11 C C7 16C . . . R 5 -11.77 -33.594 46.99 1 111.42 ? C7 16C 409 B 1 HETATM 12 C C8 16C . . . R 5 -11.736 -32.083 47.354 1 102.73 ? C8 16C 409 B 1 HETATM 13 C C9 16C . . . R 5 -11.473 -31.256 46.079 1 88.89 ? C9 16C 409 B 1 HETATM 14 C C10 16C . . . R 5 -11.935 -29.79 46.288 1 120.55 ? C10 16C 409 B 1 HETATM 15 C C11 16C . . . R 5 -10.794 -28.832 45.911 1 111.81 ? C11 16C 409 B 1 HETATM 16 C C12 16C . . . R 5 -11.362 -27.551 45.256 1 110.88 ? C12 16C 409 B 1 HETATM 17 C C13 16C . . . R 5 -10.314 -26.983 44.258 1 98.11 ? C13 16C 409 B 1 HETATM 18 C C14 16C . . . R 5 -10.804 -25.638 43.653 1 89.56 ? C14 16C 409 B 1 HETATM 19 C C15 16C . . . R 5 -11.067 -24.624 44.789 1 110.53 ? C15 16C 409 B 1 HETATM 20 C C16 16C . . . R 5 -10.984 -23.189 44.243 1 94.82 ? C16 16C 409 B 1 HETATM 21 C C17 16C . . . R 5 -11.942 -22.282 45.041 1 92.27 ? C17 16C 409 B 1 HETATM 22 C C18 16C . . . R 5 -11.244 -20.965 45.403 1 73.54 ? C18 16C 409 B 1 HETATM 23 O O3 16C . . . R 5 -8.91 -37.472 47.763 1 134.72 ? O3 16C 409 B 1 HETATM 24 C C20 16C . . . R 5 -6.118 -31.983 48.005 1 101.97 ? C20 16C 409 B 1 HETATM 25 C C21 16C . . . R 5 -6.701 -30.825 47.161 1 83.53 ? C21 16C 409 B 1 HETATM 26 C C22 16C . . . R 5 -6.253 -29.47 47.751 1 82.92 ? C22 16C 409 B 1 HETATM 27 C C23 16C . . . R 5 -7.158 -28.355 47.169 1 90.27 ? C23 16C 409 B 1 HETATM 28 C C24 16C . . . R 5 -6.358 -27.025 47.071 1 96.72 ? C24 16C 409 B 1 HETATM 29 C C25 16C . . . R 5 -7.048 -25.929 47.934 1 78.74 ? C25 16C 409 B 1 HETATM 30 C C26 16C . . . R 5 -6.296 -24.586 47.751 1 99.33 ? C26 16C 409 B 1 HETATM 31 C C27 16C . . . R 5 -7.301 -23.397 47.878 1 110.99 ? C27 16C 409 B 1 HETATM 32 C C28 16C . . . R 5 -6.567 -22.059 47.638 1 105.68 ? C28 16C 409 B 1 HETATM 33 C C29 16C . . . R 5 -7.598 -20.973 47.227 1 138.94 ? C29 16C 409 B 1 HETATM 34 C C30 16C . . . R 5 -6.927 -19.587 47.235 1 137.52 ? C30 16C 409 B 1 HETATM 35 C C31 16C . . . R 5 -7.377 -18.786 48.474 1 148.2 ? C31 16C 409 B 1 HETATM 36 C C32 16C . . . R 5 -6.527 -17.5 48.605 1 134.26 ? C32 16C 409 B 1 HETATM 37 C C33 16C . . . R 5 -6.828 -16.804 49.926 1 123.47 ? C33 16C 409 B 1 HETATM 38 C C34 16C . . . R 5 -5.729 -15.771 50.22 1 108.21 ? C34 16C 409 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 38 #