data_6W8F # _model_server_result.job_id p-qcWaR_uw20QCWe2zslVg _model_server_result.datetime_utc '2024-11-26 13:15:13' _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 6w8f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":403}' # _entry.id 6W8F # _exptl.entry_id 6W8F _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 6W8F _cell.length_a 66.671 _cell.length_b 119.963 _cell.length_c 128.941 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6W8F _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 _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 E _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 74 A CYS 93 1_555 B SG CYS 74 B CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc1 A O THR 123 A THR 142 1_555 C K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc2 A O THR 123 A THR 142 1_555 J K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.02 ? metalc ? metalc3 A OG1 THR 123 A THR 142 1_555 J K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.319 ? metalc ? metalc4 A O ILE 124 A ILE 143 1_555 C K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc5 A O ILE 124 A ILE 143 1_555 I K K . A K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? metalc ? metalc6 A O GLY 125 A GLY 144 1_555 I K K . A K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc7 A O GLY 125 A GLY 144 1_555 M K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc8 A O PHE 126 A PHE 145 1_555 M K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc9 A O THR 232 A THR 251 1_555 C K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc10 A O THR 232 A THR 251 1_555 J K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? metalc ? metalc11 A OG1 THR 232 A THR 251 1_555 J K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.199 ? metalc ? metalc12 A O ILE 233 A ILE 252 1_555 C K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc13 A O ILE 233 A ILE 252 1_555 I K K . A K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? metalc ? metalc14 A O GLY 234 A GLY 253 1_555 I K K . A K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc15 A O GLY 234 A GLY 253 1_555 M K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.007 ? metalc ? metalc16 A O PHE 235 A PHE 254 1_555 M K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc17 C K K . A K 401 1_555 B O THR 123 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc18 C K K . A K 401 1_555 B O ILE 124 B ILE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? metalc ? metalc19 C K K . A K 401 1_555 B O THR 232 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc20 C K K . A K 401 1_555 B O ILE 233 B ILE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc21 I K K . A K 407 1_555 B O ILE 124 B ILE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc22 I K K . A K 407 1_555 B O GLY 125 B GLY 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc23 I K K . A K 407 1_555 B O ILE 233 B ILE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? metalc ? metalc24 I K K . A K 407 1_555 B O GLY 234 B GLY 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc25 J K K . A K 408 1_555 B O THR 123 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.008 ? metalc ? metalc26 J K K . A K 408 1_555 B OG1 THR 123 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.234 ? metalc ? metalc27 J K K . A K 408 1_555 B O THR 232 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc28 J K K . A K 408 1_555 B OG1 THR 232 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.042 ? metalc ? metalc29 B O GLY 125 B GLY 144 1_555 M K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc30 B O PHE 126 B PHE 145 1_555 M K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? metalc ? metalc31 B O GLY 234 B GLY 253 1_555 M K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc32 B O PHE 235 B PHE 254 1_555 M K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? # _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 6W8F _atom_sites.fract_transf_matrix[1][1] 0.014999 _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] 0.008336 _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] 0.007755 _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 K A 1 401 403 K K . D 3 Q6F A 1 402 406 Q6F Q6F . E 4 16C A 1 403 407 16C 16C . F 5 R16 A 1 404 408 R16 R16 . G 5 R16 A 1 405 409 R16 R16 . H 5 R16 A 1 406 410 R16 R16 . I 2 K A 1 407 401 K K . J 2 K A 1 408 402 K K . K 6 CD A 1 409 1 CD CD . L 7 LNK A 1 410 1 LNK LNK . M 2 K B 1 401 402 K K . N 5 R16 B 1 402 404 R16 R16 . O 6 CD B 1 403 404 CD CD . P 6 CD B 1 404 405 CD CD . Q 6 CD B 1 405 406 CD CD . R 5 R16 B 1 406 407 R16 R16 . S 5 R16 B 1 407 408 R16 R16 . T 5 R16 B 1 408 409 R16 R16 . U 3 Q6F B 1 409 410 Q6F Q6F . V 5 R16 B 1 410 411 R16 R16 . W 5 R16 B 1 411 412 R16 R16 . X 8 D12 B 1 412 1 D12 D12 . # 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 . . . E 4 23.437 -15.716 -12.8 1 149.59 ? O19 16C 403 A 1 HETATM 2 C C19 16C . . . E 4 22.829 -15.231 -11.906 1 149.61 ? C19 16C 403 A 1 HETATM 3 N N2 16C . . . E 4 23.434 -15.124 -10.56 1 150.93 ? N2 16C 403 A 1 HETATM 4 C C2 16C . . . E 4 24.782 -15.611 -10.319 1 152.89 ? C2 16C 403 A 1 HETATM 5 C C1 16C . . . E 4 25.721 -14.42 -10.099 1 155.61 ? C1 16C 403 A 1 HETATM 6 O O1 16C . . . E 4 27.016 -14.893 -9.778 1 158.08 ? O1 16C 403 A 1 HETATM 7 C C3 16C . . . E 4 24.776 -16.501 -9.069 1 151.38 ? C3 16C 403 A 1 HETATM 8 C C4 16C . . . E 4 23.817 -17.682 -9.296 1 148.13 ? C4 16C 403 A 1 HETATM 9 C C5 16C . . . E 4 23.524 -18.543 -8.273 1 142.79 ? C5 16C 403 A 1 HETATM 10 C C6 16C . . . E 4 22.554 -19.722 -8.528 1 137.57 ? C6 16C 403 A 1 HETATM 11 C C7 16C . . . E 4 21.112 -19.158 -8.731 1 132.71 ? C7 16C 403 A 1 HETATM 12 C C8 16C . . . E 4 20.724 -18.265 -7.528 1 129.18 ? C8 16C 403 A 1 HETATM 13 C C9 16C . . . E 4 19.194 -18.312 -7.327 1 127.05 ? C9 16C 403 A 1 HETATM 14 C C10 16C . . . E 4 18.778 -19.728 -6.875 1 126.86 ? C10 16C 403 A 1 HETATM 15 C C11 16C . . . E 4 17.88 -20.402 -7.973 1 128.11 ? C11 16C 403 A 1 HETATM 16 C C12 16C . . . E 4 16.453 -19.786 -7.927 1 129.25 ? C12 16C 403 A 1 HETATM 17 C C13 16C . . . E 4 15.465 -20.693 -8.733 1 130.85 ? C13 16C 403 A 1 HETATM 18 C C14 16C . . . E 4 14.136 -20.818 -7.935 1 132.73 ? C14 16C 403 A 1 HETATM 19 C C15 16C . . . E 4 13.028 -21.399 -8.85 1 135.15 ? C15 16C 403 A 1 HETATM 20 C C16 16C . . . E 4 11.754 -21.699 -7.985 1 137.54 ? C16 16C 403 A 1 HETATM 21 C C17 16C . . . E 4 10.63 -22.282 -8.893 1 139.46 ? C17 16C 403 A 1 HETATM 22 C C18 16C . . . E 4 9.359 -21.406 -8.76 1 140.31 ? C18 16C 403 A 1 HETATM 23 O O3 16C . . . E 4 26.056 -16.976 -8.834 1 152.26 ? O3 16C 403 A 1 HETATM 24 C C20 16C . . . E 4 21.383 -14.704 -12.137 1 145.89 ? C20 16C 403 A 1 HETATM 25 C C21 16C . . . E 4 20.366 -15.652 -11.426 1 141.35 ? C21 16C 403 A 1 HETATM 26 C C22 16C . . . E 4 19.198 -14.795 -10.809 1 137.19 ? C22 16C 403 A 1 HETATM 27 C C23 16C . . . E 4 17.817 -15.49 -11.149 1 133.8 ? C23 16C 403 A 1 HETATM 28 C C24 16C . . . E 4 16.851 -15.429 -9.896 1 130.77 ? C24 16C 403 A 1 HETATM 29 C C25 16C . . . E 4 15.518 -16.226 -10.236 1 130.78 ? C25 16C 403 A 1 HETATM 30 C C26 16C . . . E 4 14.301 -15.582 -9.467 1 134.14 ? C26 16C 403 A 1 HETATM 31 C C27 16C . . . E 4 13.417 -16.717 -8.831 1 138.74 ? C27 16C 403 A 1 HETATM 32 C C28 16C . . . E 4 12.333 -16.076 -7.914 1 142.94 ? C28 16C 403 A 1 HETATM 33 C C29 16C . . . E 4 11.53 -17.211 -7.187 1 147.23 ? C29 16C 403 A 1 HETATM 34 C C30 16C . . . E 4 11.27 -16.784 -5.707 1 150.86 ? C30 16C 403 A 1 HETATM 35 C C31 16C . . . E 4 10.864 -18.044 -4.867 1 152.95 ? C31 16C 403 A 1 HETATM 36 C C32 16C . . . E 4 11.886 -18.233 -3.706 1 155.77 ? C32 16C 403 A 1 HETATM 37 C C33 16C . . . E 4 11.918 -19.727 -3.29 1 159.41 ? C33 16C 403 A 1 HETATM 38 C C34 16C . . . E 4 13.341 -20.09 -2.775 1 161.89 ? C34 16C 403 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 385 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #