data_4APQ # _model_server_result.job_id eG47UrSxIVdAlWLpsUQukA _model_server_result.datetime_utc '2024-12-04 23:46:20' _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 4apq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1296}' # _entry.id 4APQ # _exptl.entry_id 4APQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 890.301 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE _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 4APQ _cell.length_a 95.11 _cell.length_b 95.11 _cell.length_c 291.4 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4APQ _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 8 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide 7 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 3 MAN BMA C1 O1 . O4 HO4 . sing 5 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 7 3 2 BMA NAG C1 O1 . O4 HO4 . 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 304 NAG 5 n E NAG 2 E 2 NAG A 305 NAG 6 n F NAG 1 F 1 NAG A 306 NAG 6 n F NAG 2 F 2 NAG A 307 NAG 6 n F BMA 3 F 3 BMA A 308 BMA 6 n F MAN 4 F 4 MAN A 312 MAN 7 n G NAG 1 G 1 NAG A 309 NAG 7 n G NAG 2 G 2 NAG A 310 NAG 7 n G BMA 3 G 3 BMA A 311 BMA # 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 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 C SG CYS 22 C CYS 22 1_555 C SG CYS 89 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? disulf ? disulf5 D SG CYS 23 D CYS 23 1_555 D SG CYS 91 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 D SG CYS 144 D CYS 148 1_555 D SG CYS 209 D CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale5 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale7 F O4 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale8 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale9 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? # _chem_comp.formula 'C48 H91 N O11 S' _chem_comp.formula_weight 890.301 _chem_comp.id CIS _chem_comp.mon_nstd_flag . _chem_comp.name (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL;CIS-TETRACOSENOYL SULFATIDE' # 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 C17 C16 CIS sing 94 n n C17 H171 CIS sing 95 n n C17 H172 CIS sing 96 n n C17 H173 CIS sing 97 n n C16 C15 CIS sing 98 n n C16 H161 CIS sing 99 n n C16 H162 CIS sing 100 n n C15 C14 CIS sing 101 n n C15 H151 CIS sing 102 n n C15 H152 CIS sing 103 n n C14 C13 CIS sing 104 n n C14 H141 CIS sing 105 n n C14 H142 CIS sing 106 n n C13 C12 CIS sing 107 n n C13 H131 CIS sing 108 n n C13 H132 CIS sing 109 n n C12 C11 CIS sing 110 n n C12 H121 CIS sing 111 n n C12 H122 CIS sing 112 n n C11 C10 CIS sing 113 n n C11 H111 CIS sing 114 n n C11 H112 CIS sing 115 n n C10 C9 CIS sing 116 n n C10 H101 CIS sing 117 n n C10 H102 CIS sing 118 n n C9 C8 CIS sing 119 n n C9 H91 CIS sing 120 n n C9 H92 CIS sing 121 n n C8 C7 CIS sing 122 n n C8 H81 CIS sing 123 n n C8 H82 CIS sing 124 n n C7 C6 CIS sing 125 n n C7 H71 CIS sing 126 n n C7 H72 CIS sing 127 n n C6 C5 CIS sing 128 n n C6 H61 CIS sing 129 n n C6 H62 CIS sing 130 n n C5 C4 CIS sing 131 n n C5 H51 CIS sing 132 n n C5 H52 CIS sing 133 n n C4 C3 CIS doub 134 e n C4 H4 CIS sing 135 n n C3 C2 CIS sing 136 n n C3 H3 CIS sing 137 n n C2 O1 CIS sing 138 n n C2 C1 CIS sing 139 n n C2 H2 CIS sing 140 n n O1 HO1 CIS sing 141 n n C1 C CIS sing 142 n n C1 N CIS sing 143 n n C1 H1 CIS sing 144 n n C O CIS sing 145 n n C H1A CIS sing 146 n n C H2A CIS sing 147 n n O C43 CIS sing 148 n n C43 C44 CIS sing 149 n n C43 O6 CIS sing 150 n n C43 H43 CIS sing 151 n n C44 O3 CIS sing 152 n n C44 C45 CIS sing 153 n n C44 H44 CIS sing 154 n n O3 HO3 CIS sing 155 n n O6 C47 CIS sing 156 n n C47 C48 CIS sing 157 n n C47 C46 CIS sing 158 n n C47 H47 CIS sing 159 n n C48 O7 CIS sing 160 n n C48 H481 CIS sing 161 n n C48 H482 CIS sing 162 n n O7 HO7 CIS sing 163 n n C46 O5 CIS sing 164 n n C46 C45 CIS sing 165 n n C46 H46 CIS sing 166 n n O5 HO5 CIS sing 167 n n C45 O4 CIS sing 168 n n C45 H45 CIS sing 169 n n O4 S CIS sing 170 n n S O10 CIS sing 171 n n S O9 CIS doub 172 n n S O8 CIS doub 173 n n O10 H10 CIS sing 174 n n N C18 CIS sing 175 n n N HN CIS sing 176 n n C18 O2 CIS doub 177 n n C18 C19 CIS sing 178 n n C19 C20 CIS sing 179 n n C19 H191 CIS sing 180 n n C19 H192 CIS sing 181 n n C20 C21 CIS sing 182 n n C20 H201 CIS sing 183 n n C20 H202 CIS sing 184 n n C21 C22 CIS sing 185 n n C21 H211 CIS sing 186 n n C21 H212 CIS sing 187 n n C22 C23 CIS sing 188 n n C22 H221 CIS sing 189 n n C22 H222 CIS sing 190 n n C23 C24 CIS sing 191 n n C23 H231 CIS sing 192 n n C23 H232 CIS sing 193 n n C24 C25 CIS sing 194 n n C24 H241 CIS sing 195 n n C24 H242 CIS sing 196 n n C25 C26 CIS sing 197 n n C25 H251 CIS sing 198 n n C25 H252 CIS sing 199 n n C26 C27 CIS sing 200 n n C26 H261 CIS sing 201 n n C26 H262 CIS sing 202 n n C27 C28 CIS sing 203 n n C27 H271 CIS sing 204 n n C27 H272 CIS sing 205 n n C28 C29 CIS sing 206 n n C28 H281 CIS sing 207 n n C28 H282 CIS sing 208 n n C29 C30 CIS sing 209 n n C29 H291 CIS sing 210 n n C29 H292 CIS sing 211 n n C30 C31 CIS sing 212 n n C30 H301 CIS sing 213 n n C30 H302 CIS sing 214 n n C31 C32 CIS sing 215 n n C31 H311 CIS sing 216 n n C31 H312 CIS sing 217 n n C32 C33 CIS doub 218 z n C32 H32 CIS sing 219 n n C33 C34 CIS sing 220 n n C33 H33 CIS sing 221 n n C34 C35 CIS sing 222 n n C34 H341 CIS sing 223 n n C34 H342 CIS sing 224 n n C35 C36 CIS sing 225 n n C35 H351 CIS sing 226 n n C35 H352 CIS sing 227 n n C36 C37 CIS sing 228 n n C36 H361 CIS sing 229 n n C36 H362 CIS sing 230 n n C37 C38 CIS sing 231 n n C37 H371 CIS sing 232 n n C37 H372 CIS sing 233 n n C38 C39 CIS sing 234 n n C38 H381 CIS sing 235 n n C38 H382 CIS sing 236 n n C39 C40 CIS sing 237 n n C39 H391 CIS sing 238 n n C39 H392 CIS sing 239 n n C40 C41 CIS sing 240 n n C40 H401 CIS sing 241 n n C40 H402 CIS sing 242 n n C41 H411 CIS sing 243 n n C41 H412 CIS sing 244 n n C41 H413 CIS sing 245 n n # _atom_sites.entry_id 4APQ _atom_sites.fract_transf_matrix[1][1] 0.010514 _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] 0.010514 _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] 0.003432 _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 H 8 CIS A 1 1296 1296 CIS CIS . I 9 HOH A 1 2001 2001 HOH HOH . J 9 HOH B 1 2001 2001 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 CIS . . . H 8 -0.884 -95.014 -53.926 1 142.26 ? C1 CIS 1296 A 1 HETATM 2 C C CIS . . . H 8 -2.089 -94.14 -53.528 1 147.53 ? C CIS 1296 A 1 HETATM 3 O O CIS . . . H 8 -2.314 -92.966 -54.358 1 154.6 ? O CIS 1296 A 1 HETATM 4 C C43 CIS . . . H 8 -1.454 -92.877 -55.526 1 162.42 ? C43 CIS 1296 A 1 HETATM 5 C C44 CIS . . . H 8 -1.801 -91.579 -56.283 1 165.83 ? C44 CIS 1296 A 1 HETATM 6 O O3 CIS . . . H 8 -3.188 -91.551 -56.648 1 164.22 ? O3 CIS 1296 A 1 HETATM 7 O O6 CIS . . . H 8 -0.052 -92.899 -55.163 1 165.65 ? O6 CIS 1296 A 1 HETATM 8 C C47 CIS . . . H 8 0.793 -92.831 -56.333 1 166.9 ? C47 CIS 1296 A 1 HETATM 9 C C48 CIS . . . H 8 2.265 -92.933 -55.886 1 165.71 ? C48 CIS 1296 A 1 HETATM 10 O O7 CIS . . . H 8 3.039 -91.805 -56.306 1 165.01 ? O7 CIS 1296 A 1 HETATM 11 C C46 CIS . . . H 8 0.555 -91.513 -57.1 1 169.57 ? C46 CIS 1296 A 1 HETATM 12 O O5 CIS . . . H 8 0.884 -90.378 -56.289 1 170.36 ? O5 CIS 1296 A 1 HETATM 13 C C45 CIS . . . H 8 -0.921 -91.455 -57.537 1 170.3 ? C45 CIS 1296 A 1 HETATM 14 O O4 CIS . . . H 8 -1.214 -90.224 -58.241 1 173.64 ? O4 CIS 1296 A 1 HETATM 15 S S CIS . . . H 8 -0.808 -90.303 -59.728 1 175.07 ? S CIS 1296 A 1 HETATM 16 O O10 CIS . . . H 8 -1.905 -89.764 -60.452 1 175.42 ? O10 CIS 1296 A 1 HETATM 17 O O9 CIS . . . H 8 -0.255 -91.59 -59.972 1 177.01 ? O9 CIS 1296 A 1 HETATM 18 O O8 CIS . . . H 8 0.341 -89.317 -59.927 1 173.82 ? O8 CIS 1296 A 1 HETATM 19 N N CIS . . . H 8 -1.252 -96.064 -54.88 1 136.99 ? N CIS 1296 A 1 HETATM 20 C C18 CIS . . . H 8 -0.352 -97.017 -55.22 1 133.05 ? C18 CIS 1296 A 1 HETATM 21 O O2 CIS . . . H 8 0.762 -97.029 -54.736 1 130.38 ? O2 CIS 1296 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #