data_3SDA # _model_server_result.job_id EG9xXdazy1S6h4TIvRIRTQ _model_server_result.datetime_utc '2024-10-12 11:15:27' _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 3sda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":601}' # _entry.id 3SDA # _exptl.entry_id 3SDA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 812.254 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide _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 3SDA _cell.length_a 94.75 _cell.length_b 94.75 _cell.length_c 287.52 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SDA _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 _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 7 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 5 n E NAG 1 E 1 NAG A 305 NAG 5 n E NAG 2 E 2 NAG A 306 NAG # 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 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? disulf ? disulf2 C SG CYS 161 C CYS 164 1_555 D SG CYS 172 D CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? disulf ? disulf3 D SG CYS 25 D CYS 23 1_555 D SG CYS 93 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? disulf ? disulf4 D SG CYS 146 D CYS 148 1_555 D SG CYS 211 D CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 F C1 NAG . A NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 G C1 NAG . A NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.201 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? # _chem_comp.formula 'C48 H93 N O8' _chem_comp.formula_weight 812.254 _chem_comp.id GCY _chem_comp.mon_nstd_flag . _chem_comp.name N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'beta-Galactosylceramide, Ceramide beta-D-galactoside' # _atom_sites.entry_id 3SDA _atom_sites.fract_transf_matrix[1][1] 0.010554 _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] 0.010554 _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] 0.003478 _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 F 6 NAG A 1 303 303 NAG NAG . G 6 NAG A 1 304 304 NAG NAG . H 7 GCY A 1 601 601 GCY DRG . I 8 GOL B 1 100 100 GOL GOL . J 9 HOH A 1 307 2 HOH HOH . J 9 HOH A 2 308 7 HOH HOH . J 9 HOH A 3 309 11 HOH HOH . J 9 HOH A 4 310 25 HOH HOH . J 9 HOH A 5 311 41 HOH HOH . J 9 HOH A 6 312 50 HOH HOH . J 9 HOH A 7 313 54 HOH HOH . J 9 HOH A 8 314 57 HOH HOH . J 9 HOH A 9 315 67 HOH HOH . J 9 HOH A 10 316 68 HOH HOH . J 9 HOH A 11 317 75 HOH HOH . J 9 HOH A 12 318 112 HOH HOH . J 9 HOH A 13 319 113 HOH HOH . J 9 HOH A 14 320 117 HOH HOH . J 9 HOH A 15 321 118 HOH HOH . J 9 HOH A 16 322 119 HOH HOH . J 9 HOH A 17 323 122 HOH HOH . J 9 HOH A 18 324 124 HOH HOH . J 9 HOH A 19 325 125 HOH HOH . K 9 HOH B 1 101 46 HOH HOH . K 9 HOH B 2 102 59 HOH HOH . K 9 HOH B 3 103 79 HOH HOH . K 9 HOH B 4 104 80 HOH HOH . K 9 HOH B 5 105 81 HOH HOH . K 9 HOH B 6 106 83 HOH HOH . K 9 HOH B 7 107 84 HOH HOH . K 9 HOH B 8 108 86 HOH HOH . K 9 HOH B 9 109 88 HOH HOH . K 9 HOH B 10 110 89 HOH HOH . K 9 HOH B 11 114 114 HOH HOH . K 9 HOH B 12 121 121 HOH HOH . L 9 HOH C 1 211 1 HOH HOH . L 9 HOH C 2 212 3 HOH HOH . L 9 HOH C 3 213 6 HOH HOH . L 9 HOH C 4 214 16 HOH HOH . L 9 HOH C 5 215 21 HOH HOH . L 9 HOH C 6 216 24 HOH HOH . L 9 HOH C 7 217 28 HOH HOH . L 9 HOH C 8 218 36 HOH HOH . L 9 HOH C 9 219 37 HOH HOH . L 9 HOH C 10 220 47 HOH HOH . L 9 HOH C 11 221 90 HOH HOH . L 9 HOH C 12 222 92 HOH HOH . L 9 HOH C 13 223 95 HOH HOH . L 9 HOH C 14 224 96 HOH HOH . L 9 HOH C 15 225 98 HOH HOH . L 9 HOH C 16 226 123 HOH HOH . M 9 HOH D 1 248 4 HOH HOH . M 9 HOH D 2 249 10 HOH HOH . M 9 HOH D 3 250 20 HOH HOH . M 9 HOH D 4 251 22 HOH HOH . M 9 HOH D 5 252 27 HOH HOH . M 9 HOH D 6 253 30 HOH HOH . M 9 HOH D 7 254 56 HOH HOH . M 9 HOH D 8 255 64 HOH HOH . M 9 HOH D 9 256 97 HOH HOH . M 9 HOH D 10 257 99 HOH HOH . M 9 HOH D 11 258 100 HOH HOH . M 9 HOH D 12 259 105 HOH HOH . M 9 HOH D 13 260 110 HOH HOH . M 9 HOH D 14 261 120 HOH HOH . M 9 HOH D 15 262 126 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 C1 GCY . . . H 7 -15.8 -99.248 -45.971 1 56.59 ? C1 GCY 601 A 1 HETATM 2 N N1 GCY . . . H 7 -2.667 -94.683 -53.719 1 60.29 ? N1 GCY 601 A 1 HETATM 3 O O1 GCY . . . H 7 -5.158 -94.126 -51.298 1 60.07 ? O1 GCY 601 A 1 HETATM 4 C C2 GCY . . . H 7 -15.163 -100.58 -46.373 1 56.76 ? C2 GCY 601 A 1 HETATM 5 O O2 GCY . . . H 7 -2.963 -91.321 -53.616 1 65.28 ? O2 GCY 601 A 1 HETATM 6 C C3 GCY . . . H 7 -14.227 -100.403 -47.572 1 57.06 ? C3 GCY 601 A 1 HETATM 7 O O3 GCY . . . H 7 0.96 -89.587 -55.791 1 67.05 ? O3 GCY 601 A 1 HETATM 8 C C4 GCY . . . H 7 -13.894 -101.751 -48.216 1 56.83 ? C4 GCY 601 A 1 HETATM 9 O O4 GCY . . . H 7 -1.216 -90.714 -55.257 1 67.32 ? O4 GCY 601 A 1 HETATM 10 C C5 GCY . . . H 7 -12.383 -101.965 -48.304 1 57.17 ? C5 GCY 601 A 1 HETATM 11 O O5 GCY . . . H 7 -1.834 -89.268 -57.811 1 68.43 ? O5 GCY 601 A 1 HETATM 12 C C6 GCY . . . H 7 -11.939 -102.224 -49.751 1 57.47 ? C6 GCY 601 A 1 HETATM 13 C C7 GCY . . . H 7 -10.906 -101.188 -50.206 1 57.09 ? C7 GCY 601 A 1 HETATM 14 C C8 GCY . . . H 7 -9.992 -101.759 -51.292 1 57.25 ? C8 GCY 601 A 1 HETATM 15 C C9 GCY . . . H 7 -8.516 -101.541 -50.935 1 57.59 ? C9 GCY 601 A 1 HETATM 16 C C10 GCY . . . H 7 -7.944 -100.286 -51.602 1 57.49 ? C10 GCY 601 A 1 HETATM 17 C C11 GCY . . . H 7 -6.439 -100.159 -51.34 1 57.83 ? C11 GCY 601 A 1 HETATM 18 C C12 GCY . . . H 7 -5.809 -99.04 -52.178 1 58.01 ? C12 GCY 601 A 1 HETATM 19 C C13 GCY . . . H 7 -5.729 -97.741 -51.373 1 58.72 ? C13 GCY 601 A 1 HETATM 20 C C14 GCY . . . H 7 -6.022 -96.523 -52.249 1 59.05 ? C14 GCY 601 A 1 HETATM 21 C C15 GCY . . . H 7 -4.843 -95.855 -52.558 1 59.82 ? C15 GCY 601 A 1 HETATM 22 C C16 GCY . . . H 7 -4.701 -94.475 -52.403 1 60.48 ? C16 GCY 601 A 1 HETATM 23 O O16 GCY . . . H 7 -4.147 -90.659 -58.226 1 69.39 ? O16 GCY 601 A 1 HETATM 24 C C17 GCY . . . H 7 -3.381 -93.788 -52.778 1 61.18 ? C17 GCY 601 A 1 HETATM 25 O O17 GCY . . . H 7 -4.791 -91.495 -55.599 1 67.96 ? O17 GCY 601 A 1 HETATM 26 C C18 GCY . . . H 7 -3.811 -92.466 -53.409 1 62.96 ? C18 GCY 601 A 1 HETATM 27 O O18 GCY . . . H 7 -0.602 -94.359 -52.814 1 59.34 ? O18 GCY 601 A 1 HETATM 28 C C19 GCY . . . H 7 -2.465 -91.388 -54.975 1 66.77 ? C19 GCY 601 A 1 HETATM 29 C C20 GCY . . . H 7 -0.725 -91.117 -56.614 1 67.81 ? C20 GCY 601 A 1 HETATM 30 C C21 GCY . . . H 7 0.604 -90.42 -56.903 1 67.62 ? C21 GCY 601 A 1 HETATM 31 C C22 GCY . . . H 7 -1.79 -90.698 -57.708 1 68.04 ? C22 GCY 601 A 1 HETATM 32 C C35 GCY . . . H 7 -3.183 -91.228 -57.349 1 68.11 ? C35 GCY 601 A 1 HETATM 33 C C36 GCY . . . H 7 -3.536 -90.894 -55.933 1 67.62 ? C36 GCY 601 A 1 HETATM 34 C C37 GCY . . . H 7 -1.352 -94.913 -53.62 1 59.4 ? C37 GCY 601 A 1 HETATM 35 C C38 GCY . . . H 7 -0.805 -95.93 -54.641 1 58.54 ? C38 GCY 601 A 1 HETATM 36 C C39 GCY . . . H 7 0.032 -97.043 -53.972 1 58.41 ? C39 GCY 601 A 1 HETATM 37 C C40 GCY . . . H 7 -0.791 -98.269 -53.51 1 58.18 ? C40 GCY 601 A 1 HETATM 38 C C41 GCY . . . H 7 0.119 -99.417 -53.009 1 58.06 ? C41 GCY 601 A 1 HETATM 39 C C42 GCY . . . H 7 -0.634 -100.501 -52.205 1 58 ? C42 GCY 601 A 1 HETATM 40 C C43 GCY . . . H 7 0.321 -101.563 -51.62 1 58.21 ? C43 GCY 601 A 1 HETATM 41 C C44 GCY . . . H 7 -0.14 -102.081 -50.243 1 58.79 ? C44 GCY 601 A 1 HETATM 42 C CAJ GCY . . . H 7 0.952 -102.91 -49.529 1 59.52 ? CAJ GCY 601 A 1 HETATM 43 C CAK GCY . . . H 7 1.368 -102.308 -48.166 1 60.2 ? CAK GCY 601 A 1 HETATM 44 C CAL GCY . . . H 7 2.793 -102.728 -47.745 1 60.24 ? CAL GCY 601 A 1 HETATM 45 C CAM GCY . . . H 7 3.305 -101.946 -46.524 1 59.43 ? CAM GCY 601 A 1 HETATM 46 C CAN GCY . . . H 7 4.622 -102.304 -46.403 1 30 ? CAN GCY 601 A 1 HETATM 47 C CAO GCY . . . H 7 5.781 -102.591 -47.301 1 30 ? CAO GCY 601 A 1 HETATM 48 C CAP GCY . . . H 7 7.224 -103.008 -46.694 1 30 ? CAP GCY 601 A 1 HETATM 49 C CAQ GCY . . . H 7 8.277 -102.826 -47.527 1 30 ? CAQ GCY 601 A 1 HETATM 50 C CAR GCY . . . H 7 8.677 -103.909 -48.324 1 30 ? CAR GCY 601 A 1 HETATM 51 C CAS GCY . . . H 7 9.19 -103.658 -49.689 1 30 ? CAS GCY 601 A 1 HETATM 52 C CAT GCY . . . H 7 8.409 -104.402 -50.582 1 30 ? CAT GCY 601 A 1 HETATM 53 C CAU GCY . . . H 7 8.18 -103.993 -51.939 1 30 ? CAU GCY 601 A 1 HETATM 54 C CAV GCY . . . H 7 7.462 -104.641 -53.005 1 30 ? CAV GCY 601 A 1 HETATM 55 C CAW GCY . . . H 7 6.038 -104.73 -52.615 1 30 ? CAW GCY 601 A 1 HETATM 56 C CAX GCY . . . H 7 5.296 -105.17 -53.189 1 30 ? CAX GCY 601 A 1 HETATM 57 C CAY GCY . . . H 7 4.072 -105.612 -53.219 1 30 ? CAY GCY 601 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 57 #