data_6W8A # _model_server_result.job_id 6mNH3qJGo5FMM6cJNzCExQ _model_server_result.datetime_utc '2025-01-31 14:54:27' _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 6w8a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":404}' # _entry.id 6W8A # _exptl.entry_id 6W8A _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 6W8A _cell.length_a 66.867 _cell.length_b 119.951 _cell.length_c 129.245 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6W8A _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 74 A CYS 93 1_555 B SG CYS 74 B CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A O THR 123 A THR 142 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc2 A O THR 123 A THR 142 1_555 J K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? metalc ? metalc3 A OG1 THR 123 A THR 142 1_555 J K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.361 ? metalc ? metalc4 A O ILE 124 A ILE 143 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? metalc ? metalc5 A O ILE 124 A ILE 143 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc6 A O GLY 125 A GLY 144 1_555 C K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc7 A O GLY 125 A GLY 144 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? metalc ? metalc8 A O PHE 126 A PHE 145 1_555 C K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc9 A O THR 232 A THR 251 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? metalc ? metalc10 A O THR 232 A THR 251 1_555 J K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc11 A OG1 THR 232 A THR 251 1_555 J K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.047 ? metalc ? metalc12 A O ILE 233 A ILE 252 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc13 A O ILE 233 A ILE 252 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc14 A O GLY 234 A GLY 253 1_555 C K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc15 A O GLY 234 A GLY 253 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? metalc ? metalc16 A O PHE 235 A PHE 254 1_555 C K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc17 A OE1 GLU 290 A GLU 309 1_555 P CD CD . B CD 404 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc18 C K K . A K 401 1_555 B O GLY 125 B GLY 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc19 C K K . A K 401 1_555 B O PHE 126 B PHE 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? metalc ? metalc20 C K K . A K 401 1_555 B O GLY 234 B GLY 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc21 C K K . A K 401 1_555 B O PHE 235 B PHE 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc22 D K K . A K 402 1_555 B O THR 123 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc23 D K K . A K 402 1_555 B O ILE 124 B ILE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc24 D K K . A K 402 1_555 B O THR 232 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc25 D K K . A K 402 1_555 B O ILE 233 B ILE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? metalc ? metalc26 J K K . A K 408 1_555 B O THR 123 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.051 ? metalc ? metalc27 J K K . A K 408 1_555 B OG1 THR 123 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.226 ? metalc ? metalc28 J K K . A K 408 1_555 B O THR 232 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc29 J K K . A K 408 1_555 B OG1 THR 232 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.128 ? metalc ? metalc30 B OD1 ASN 92 B ASN 111 1_555 Y K K . B K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.299 ? metalc ? metalc31 B O ILE 124 B ILE 143 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc32 B O GLY 125 B GLY 144 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc33 B O ILE 233 B ILE 252 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc34 B O GLY 234 B GLY 253 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc35 B OE1 GLU 290 B GLU 309 1_555 P CD CD . B CD 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? # _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 6W8A _atom_sites.fract_transf_matrix[1][1] 0.014955 _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] 0.008337 _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] 0.007737 _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 1 401 402 K K . D 2 K A 1 402 403 K K . E 3 Q6F A 1 403 406 Q6F Q6F . F 4 16C A 1 404 407 16C 16C . G 5 R16 A 1 405 408 R16 R16 . H 5 R16 A 1 406 409 R16 R16 . I 5 R16 A 1 407 410 R16 R16 . 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 5 R16 B 1 401 404 R16 R16 . N 2 K B 1 402 401 K K . 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 . Y 2 K B 1 413 1 K K . # 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 23.452 -15.859 -13.007 1 142.15 ? O19 16C 404 A 1 HETATM 2 C C19 16C . . . F 4 22.872 -15.378 -12.092 1 142.16 ? C19 16C 404 A 1 HETATM 3 N N2 16C . . . F 4 23.519 -15.265 -10.766 1 143.56 ? N2 16C 404 A 1 HETATM 4 C C2 16C . . . F 4 24.878 -15.737 -10.559 1 145.57 ? C2 16C 404 A 1 HETATM 5 C C1 16C . . . F 4 25.806 -14.536 -10.339 1 147.69 ? C1 16C 404 A 1 HETATM 6 O O1 16C . . . F 4 27.024 -14.982 -9.775 1 149.41 ? O1 16C 404 A 1 HETATM 7 C C3 16C . . . F 4 24.905 -16.645 -9.32 1 147.43 ? C3 16C 404 A 1 HETATM 8 C C4 16C . . . F 4 23.996 -17.864 -9.554 1 147.07 ? C4 16C 404 A 1 HETATM 9 C C5 16C . . . F 4 23.56 -18.606 -8.489 1 146.71 ? C5 16C 404 A 1 HETATM 10 C C6 16C . . . F 4 22.645 -19.834 -8.723 1 143.8 ? C6 16C 404 A 1 HETATM 11 C C7 16C . . . F 4 21.16 -19.365 -8.838 1 139.05 ? C7 16C 404 A 1 HETATM 12 C C8 16C . . . F 4 20.771 -18.542 -7.587 1 135.14 ? C8 16C 404 A 1 HETATM 13 C C9 16C . . . F 4 19.233 -18.53 -7.441 1 132.8 ? C9 16C 404 A 1 HETATM 14 C C10 16C . . . F 4 18.749 -19.909 -6.941 1 131.96 ? C10 16C 404 A 1 HETATM 15 C C11 16C . . . F 4 17.902 -20.614 -8.06 1 131.16 ? C11 16C 404 A 1 HETATM 16 C C12 16C . . . F 4 16.497 -19.953 -8.144 1 129.86 ? C12 16C 404 A 1 HETATM 17 C C13 16C . . . F 4 15.502 -20.929 -8.856 1 128.33 ? C13 16C 404 A 1 HETATM 18 C C14 16C . . . F 4 14.121 -20.849 -8.142 1 126.97 ? C14 16C 404 A 1 HETATM 19 C C15 16C . . . F 4 13.053 -21.603 -8.976 1 126.42 ? C15 16C 404 A 1 HETATM 20 C C16 16C . . . F 4 11.882 -22.066 -8.041 1 126.56 ? C16 16C 404 A 1 HETATM 21 C C17 16C . . . F 4 10.608 -22.332 -8.896 1 128.18 ? C17 16C 404 A 1 HETATM 22 C C18 16C . . . F 4 9.532 -21.267 -8.561 1 129.98 ? C18 16C 404 A 1 HETATM 23 O O3 16C . . . F 4 26.202 -17.074 -9.086 1 148.35 ? O3 16C 404 A 1 HETATM 24 C C20 16C . . . F 4 21.415 -14.865 -12.266 1 142.03 ? C20 16C 404 A 1 HETATM 25 C C21 16C . . . F 4 20.464 -15.84 -11.506 1 141.29 ? C21 16C 404 A 1 HETATM 26 C C22 16C . . . F 4 19.266 -15.04 -10.872 1 139.35 ? C22 16C 404 A 1 HETATM 27 C C23 16C . . . F 4 17.957 -15.915 -11.029 1 136.73 ? C23 16C 404 A 1 HETATM 28 C C24 16C . . . F 4 16.824 -15.408 -10.047 1 136.01 ? C24 16C 404 A 1 HETATM 29 C C25 16C . . . F 4 15.482 -16.183 -10.397 1 138.62 ? C25 16C 404 A 1 HETATM 30 C C26 16C . . . F 4 14.261 -15.515 -9.657 1 143.71 ? C26 16C 404 A 1 HETATM 31 C C27 16C . . . F 4 13.556 -16.585 -8.746 1 148.61 ? C27 16C 404 A 1 HETATM 32 C C28 16C . . . F 4 12.466 -15.889 -7.879 1 151.78 ? C28 16C 404 A 1 HETATM 33 C C29 16C . . . F 4 11.701 -16.971 -7.041 1 153.9 ? C29 16C 404 A 1 HETATM 34 C C30 16C . . . F 4 11.52 -16.451 -5.579 1 155.75 ? C30 16C 404 A 1 HETATM 35 C C31 16C . . . F 4 11.177 -17.656 -4.637 1 157.38 ? C31 16C 404 A 1 HETATM 36 C C32 16C . . . F 4 11.692 -17.351 -3.198 1 158.91 ? C32 16C 404 A 1 HETATM 37 C C33 16C . . . F 4 12.043 -18.681 -2.48 1 161.13 ? C33 16C 404 A 1 HETATM 38 C C34 16C . . . F 4 13.312 -19.305 -3.131 1 163.72 ? C34 16C 404 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 38 #