data_1GZP # _model_server_result.job_id Y2VkvIVAPb6qOUtXFlyO9g _model_server_result.datetime_utc '2024-11-01 15:36:21' _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 1gzp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1280}' # _entry.id 1GZP # _exptl.entry_id 1GZP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 744.137 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(1S,2S)-2-HYDROXY-1-({[(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]OXY}METHYL)OCTADECYL]OCTADECANAMIDE _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 1GZP _cell.length_a 87.527 _cell.length_b 176.885 _cell.length_c 75.25 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GZP _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PQS _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 _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 3 _struct_asym.id C _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 105 A CYS 102 1_555 A SG CYS 169 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 134 A CYS 131 1_555 A SG CYS 148 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 209 A CYS 206 1_555 A SG CYS 264 A CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 26 B CYS 25 1_555 B SG CYS 81 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C43 H85 N O8' _chem_comp.formula_weight 744.137 _chem_comp.id GM2 _chem_comp.mon_nstd_flag . _chem_comp.name N-[(1S,2S)-2-HYDROXY-1-({[(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]OXY}METHYL)OCTADECYL]OCTADECANAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 O1 GM2 sing 166 n n C1 C2 GM2 sing 167 n n C1 O5 GM2 sing 168 n n C1 H1 GM2 sing 169 n n O1 CB1 GM2 sing 170 n n C2 O2 GM2 sing 171 n n C2 C3 GM2 sing 172 n n C2 H2 GM2 sing 173 n n O5 C5 GM2 sing 174 n n CB1 CB2 GM2 sing 175 n n CB1 HB11 GM2 sing 176 n n CB1 HB12 GM2 sing 177 n n O2 HA GM2 sing 178 n n C3 O3 GM2 sing 179 n n C3 C4 GM2 sing 180 n n C3 H3 GM2 sing 181 n n O3 HB GM2 sing 182 n n C4 O4 GM2 sing 183 n n C4 C5 GM2 sing 184 n n C4 H4 GM2 sing 185 n n O4 HC GM2 sing 186 n n C5 C6 GM2 sing 187 n n C5 H5 GM2 sing 188 n n C6 O6 GM2 sing 189 n n C6 H6C1 GM2 sing 190 n n C6 H6C2 GM2 sing 191 n n O6 H6 GM2 sing 192 n n CL6 CL5 GM2 sing 193 n n CL6 CL7 GM2 sing 194 n n CL6 HL61 GM2 sing 195 n n CL6 HL62 GM2 sing 196 n n CL5 CL4 GM2 sing 197 n n CL5 HL51 GM2 sing 198 n n CL5 HL52 GM2 sing 199 n n CL7 CL8 GM2 sing 200 n n CL7 HL71 GM2 sing 201 n n CL7 HL72 GM2 sing 202 n n CL4 CL3 GM2 sing 203 n n CL4 HL41 GM2 sing 204 n n CL4 HL42 GM2 sing 205 n n CL3 CL2 GM2 sing 206 n n CL3 HL31 GM2 sing 207 n n CL3 HL32 GM2 sing 208 n n CL2 CL1 GM2 sing 209 n n CL2 HL21 GM2 sing 210 n n CL2 HL22 GM2 sing 211 n n CL1 O GM2 doub 212 n n CL1 N GM2 sing 213 n n CB2 N GM2 sing 214 n n CB2 CR1 GM2 sing 215 n n CB2 HB2 GM2 sing 216 n n N H GM2 sing 217 n n CR1 OR GM2 sing 218 n n CR1 CR2 GM2 sing 219 n n CR1 HR1 GM2 sing 220 n n OR HR GM2 sing 221 n n CR2 CR3 GM2 sing 222 n n CR2 HR21 GM2 sing 223 n n CR2 HR22 GM2 sing 224 n n CR3 CR4 GM2 sing 225 n n CR3 HR31 GM2 sing 226 n n CR3 HR32 GM2 sing 227 n n CR4 CR5 GM2 sing 228 n n CR4 HR41 GM2 sing 229 n n CR4 HR42 GM2 sing 230 n n CR5 CR6 GM2 sing 231 n n CR5 HR51 GM2 sing 232 n n CR5 HR52 GM2 sing 233 n n CR6 CR7 GM2 sing 234 n n CR6 HR61 GM2 sing 235 n n CR6 HR62 GM2 sing 236 n n CR7 CR8 GM2 sing 237 n n CR7 HR71 GM2 sing 238 n n CR7 HR72 GM2 sing 239 n n CR8 CR9 GM2 sing 240 n n CR8 HR81 GM2 sing 241 n n CR8 HR82 GM2 sing 242 n n CR9 CRA GM2 sing 243 n n CR9 HR91 GM2 sing 244 n n CR9 HR92 GM2 sing 245 n n CRA CRB GM2 sing 246 n n CRA HC' GM2 sing 247 n n CRA HR11 GM2 sing 248 n n CRB CRC GM2 sing 249 n n CRB H0 GM2 sing 250 n n CRB H7 GM2 sing 251 n n CRC CRD GM2 sing 252 n n CRC H8 GM2 sing 253 n n CRC H9 GM2 sing 254 n n CRD CRE GM2 sing 255 n n CRD H10 GM2 sing 256 n n CRD H11 GM2 sing 257 n n CRE CRF GM2 sing 258 n n CRE H12 GM2 sing 259 n n CRE H13 GM2 sing 260 n n CRF CRG GM2 sing 261 n n CRF H14 GM2 sing 262 n n CRF H15 GM2 sing 263 n n CRG CRH GM2 sing 264 n n CRG H16 GM2 sing 265 n n CRG H17 GM2 sing 266 n n CRH H18 GM2 sing 267 n n CRH H19 GM2 sing 268 n n CRH H20 GM2 sing 269 n n CL8 CL9 GM2 sing 270 n n CL8 HL81 GM2 sing 271 n n CL8 HL82 GM2 sing 272 n n CL9 CLA GM2 sing 273 n n CL9 HL91 GM2 sing 274 n n CL9 HL92 GM2 sing 275 n n CLA CLB GM2 sing 276 n n CLA HL11 GM2 sing 277 n n CLA HL12 GM2 sing 278 n n CLB CLC GM2 sing 279 n n CLB H21 GM2 sing 280 n n CLB H22 GM2 sing 281 n n CLC CLD GM2 sing 282 n n CLC H23 GM2 sing 283 n n CLC H24 GM2 sing 284 n n CLD CLE GM2 sing 285 n n CLD H25 GM2 sing 286 n n CLD H26 GM2 sing 287 n n CLE CLF GM2 sing 288 n n CLE H27 GM2 sing 289 n n CLE H28 GM2 sing 290 n n CLF CLG GM2 sing 291 n n CLF H29 GM2 sing 292 n n CLF H30 GM2 sing 293 n n CLG CLH GM2 sing 294 n n CLG H31 GM2 sing 295 n n CLG H32 GM2 sing 296 n n CLH CLI GM2 sing 297 n n CLH H33 GM2 sing 298 n n CLH H34 GM2 sing 299 n n CLI H35 GM2 sing 300 n n CLI H36 GM2 sing 301 n n CLI H37 GM2 sing 302 n n # _atom_sites.entry_id 1GZP _atom_sites.fract_transf_matrix[1][1] 0.011425 _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] 0.005653 _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] 0.013289 _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 3 GM2 A 1 1280 1280 GM2 GM2 . D 4 D12 A 1 1281 1281 D12 D12 . E 5 TWT A 1 1282 1282 TWT TWT . F 6 HOH A 1 2001 2001 HOH HOH . F 6 HOH A 2 2002 2002 HOH HOH . F 6 HOH A 3 2003 2003 HOH HOH . F 6 HOH A 4 2004 2004 HOH HOH . F 6 HOH A 5 2005 2005 HOH HOH . F 6 HOH A 6 2006 2006 HOH HOH . F 6 HOH A 7 2007 2007 HOH HOH . F 6 HOH A 8 2008 2008 HOH HOH . F 6 HOH A 9 2009 2009 HOH HOH . F 6 HOH A 10 2010 2010 HOH HOH . F 6 HOH A 11 2011 2011 HOH HOH . F 6 HOH A 12 2012 2012 HOH HOH . F 6 HOH A 13 2013 2013 HOH HOH . F 6 HOH A 14 2014 2014 HOH HOH . F 6 HOH A 15 2015 2015 HOH HOH . F 6 HOH A 16 2016 2016 HOH HOH . F 6 HOH A 17 2017 2017 HOH HOH . F 6 HOH A 18 2018 2018 HOH HOH . F 6 HOH A 19 2019 2019 HOH HOH . F 6 HOH A 20 2020 2020 HOH HOH . F 6 HOH A 21 2021 2021 HOH HOH . F 6 HOH A 22 2022 2022 HOH HOH . F 6 HOH A 23 2023 2023 HOH HOH . F 6 HOH A 24 2024 2024 HOH HOH . F 6 HOH A 25 2025 2025 HOH HOH . G 6 HOH B 1 2001 2001 HOH HOH . G 6 HOH B 2 2002 2002 HOH HOH . G 6 HOH B 3 2003 2003 HOH HOH . G 6 HOH B 4 2004 2004 HOH HOH . G 6 HOH B 5 2005 2005 HOH HOH . G 6 HOH B 6 2006 2006 HOH HOH . G 6 HOH B 7 2007 2007 HOH HOH . G 6 HOH B 8 2008 2008 HOH HOH . G 6 HOH B 9 2009 2009 HOH HOH . G 6 HOH B 10 2010 2010 HOH HOH . G 6 HOH B 11 2011 2011 HOH HOH . G 6 HOH B 12 2012 2012 HOH HOH . G 6 HOH B 13 2013 2013 HOH HOH . G 6 HOH B 14 2014 2014 HOH HOH . G 6 HOH B 15 2015 2015 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 GM2 . . . C 3 72.002 12.179 -6.712 1 136.66 ? C1 GM2 1280 A 1 HETATM 2 O O1 GM2 . . . C 3 72.388 11.406 -5.617 1 132.66 ? O1 GM2 1280 A 1 HETATM 3 C C2 GM2 . . . C 3 72.92 13.408 -6.867 1 137.74 ? C2 GM2 1280 A 1 HETATM 4 O O5 GM2 . . . C 3 72.078 11.349 -7.884 1 138.52 ? O5 GM2 1280 A 1 HETATM 5 C CB1 GM2 . . . C 3 71.655 11.75 -4.464 1 125.2 ? CB1 GM2 1280 A 1 HETATM 6 O O2 GM2 . . . C 3 72.8 14.251 -5.727 1 136.92 ? O2 GM2 1280 A 1 HETATM 7 C C3 GM2 . . . C 3 72.526 14.187 -8.128 1 138.02 ? C3 GM2 1280 A 1 HETATM 8 O O3 GM2 . . . C 3 73.431 15.264 -8.333 1 137.42 ? O3 GM2 1280 A 1 HETATM 9 C C4 GM2 . . . C 3 72.53 13.258 -9.352 1 139.12 ? C4 GM2 1280 A 1 HETATM 10 O O4 GM2 . . . C 3 72.052 13.964 -10.491 1 140.4 ? O4 GM2 1280 A 1 HETATM 11 C C5 GM2 . . . C 3 71.641 12.03 -9.084 1 138.2 ? C5 GM2 1280 A 1 HETATM 12 C C6 GM2 . . . C 3 71.649 11.007 -10.216 1 136.97 ? C6 GM2 1280 A 1 HETATM 13 O O6 GM2 . . . C 3 72.819 10.198 -10.196 1 131.59 ? O6 GM2 1280 A 1 HETATM 14 C CL6 GM2 . . . C 3 65.436 16.737 -1.801 1 79.18 ? CL6 GM2 1280 A 1 HETATM 15 C CL5 GM2 . . . C 3 66.553 16.458 -2.815 1 85.65 ? CL5 GM2 1280 A 1 HETATM 16 C CL7 GM2 . . . C 3 64.424 17.749 -2.349 1 75 ? CL7 GM2 1280 A 1 HETATM 17 C CL4 GM2 . . . C 3 66.081 15.512 -3.926 1 93.56 ? CL4 GM2 1280 A 1 HETATM 18 C CL3 GM2 . . . C 3 66.638 14.101 -3.724 1 100.89 ? CL3 GM2 1280 A 1 HETATM 19 C CL2 GM2 . . . C 3 67.489 13.674 -4.92 1 110.1 ? CL2 GM2 1280 A 1 HETATM 20 C CL1 GM2 . . . C 3 68.971 13.594 -4.538 1 114.9 ? CL1 GM2 1280 A 1 HETATM 21 C CB2 GM2 . . . C 3 70.155 11.422 -4.633 1 121.11 ? CB2 GM2 1280 A 1 HETATM 22 O O GM2 . . . C 3 69.692 14.591 -4.61 1 114.1 ? O GM2 1280 A 1 HETATM 23 N N GM2 . . . C 3 69.339 12.45 -3.946 1 118.32 ? N GM2 1280 A 1 HETATM 24 C CR1 GM2 . . . C 3 69.816 10.016 -4.091 1 117.17 ? CR1 GM2 1280 A 1 HETATM 25 O OR GM2 . . . C 3 70.12 9.933 -2.694 1 119.01 ? OR GM2 1280 A 1 HETATM 26 C CR2 GM2 . . . C 3 68.341 9.634 -4.338 1 111.58 ? CR2 GM2 1280 A 1 HETATM 27 C CR3 GM2 . . . C 3 67.378 10.377 -3.395 1 102.51 ? CR3 GM2 1280 A 1 HETATM 28 C CR4 GM2 . . . C 3 67.087 9.556 -2.139 1 97.01 ? CR4 GM2 1280 A 1 HETATM 29 C CR5 GM2 . . . C 3 67.51 10.312 -0.879 1 93.86 ? CR5 GM2 1280 A 1 HETATM 30 C CR6 GM2 . . . C 3 66.328 10.512 0.071 1 89.18 ? CR6 GM2 1280 A 1 HETATM 31 C CR7 GM2 . . . C 3 66.239 11.97 0.528 1 87.01 ? CR7 GM2 1280 A 1 HETATM 32 C CR8 GM2 . . . C 3 65.373 12.103 1.773 1 82.34 ? CR8 GM2 1280 A 1 HETATM 33 C CR9 GM2 . . . C 3 65.801 13.102 2.837 1 78.23 ? CR9 GM2 1280 A 1 HETATM 34 C CRA GM2 . . . C 3 65.629 14.584 2.534 1 76.36 ? CRA GM2 1280 A 1 HETATM 35 C CRB GM2 . . . C 3 64.988 15.442 3.615 1 74.18 ? CRB GM2 1280 A 1 HETATM 36 C CRC GM2 . . . C 3 65.116 16.951 3.477 1 72.82 ? CRC GM2 1280 A 1 HETATM 37 C CRD GM2 . . . C 3 65.393 17.752 4.744 1 75.08 ? CRD GM2 1280 A 1 HETATM 38 C CRE GM2 . . . C 3 66.851 17.926 5.149 1 79.35 ? CRE GM2 1280 A 1 HETATM 39 C CRF GM2 . . . C 3 67.28 19.281 5.692 1 82.12 ? CRF GM2 1280 A 1 HETATM 40 C CRG GM2 . . . C 3 68.214 20.108 4.82 1 85.77 ? CRG GM2 1280 A 1 HETATM 41 C CRH GM2 . . . C 3 69.022 21.2 5.491 1 85.37 ? CRH GM2 1280 A 1 HETATM 42 C CL8 GM2 . . . C 3 63.531 18.29 -1.244 1 71.65 ? CL8 GM2 1280 A 1 HETATM 43 C CL9 GM2 . . . C 3 63.472 19.808 -1.077 1 68.51 ? CL9 GM2 1280 A 1 HETATM 44 C CLA GM2 . . . C 3 62.506 20.57 -1.971 1 63.77 ? CLA GM2 1280 A 1 HETATM 45 C CLB GM2 . . . C 3 62.553 22.091 -1.94 1 56.43 ? CLB GM2 1280 A 1 HETATM 46 C CLC GM2 . . . C 3 61.411 22.798 -2.65 1 52.33 ? CLC GM2 1280 A 1 HETATM 47 C CLD GM2 . . . C 3 61.467 24.305 -2.78 1 44.22 ? CLD GM2 1280 A 1 HETATM 48 C CLE GM2 . . . C 3 61.699 24.842 -4.165 1 39.51 ? CLE GM2 1280 A 1 HETATM 49 C CLF GM2 . . . C 3 60.474 25.049 -5.022 1 36.04 ? CLF GM2 1280 A 1 HETATM 50 C CLG GM2 . . . C 3 60.706 25.394 -6.476 1 31.42 ? CLG GM2 1280 A 1 HETATM 51 C CLH GM2 . . . C 3 60.206 24.416 -7.512 1 34.72 ? CLH GM2 1280 A 1 HETATM 52 C CLI GM2 . . . C 3 59.83 24.983 -8.852 1 32.02 ? CLI GM2 1280 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 52 #