data_1GZM # _model_server_result.job_id 2ZLS1V_Ccg5NtnAMwD7a4A _model_server_result.datetime_utc '2024-11-26 22:00:14' _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 1gzm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":1343}' # _entry.id 1GZM # _exptl.entry_id 1GZM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 229.402 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'LAURYL DIMETHYLAMINE-N-OXIDE' _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 1GZM _cell.length_a 103.82 _cell.length_b 103.82 _cell.length_c 76.59 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GZM _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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,Z,AA,BA,CA,DA,EA,FA,GA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 K N N ? 6 Y N N ? 6 DA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 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 2 n C NAG 1 C 1 NAG A 1335 NAG 2 n C NAG 2 C 2 NAG A 1336 NAG 2 n C BMA 3 C 3 BMA A 1337 BMA 2 n D NAG 1 D 1 NAG A 1338 NAG 2 n D NAG 2 D 2 NAG A 1339 NAG 2 n D BMA 3 D 3 BMA A 1340 BMA 2 n E NAG 1 E 1 NAG B 1335 NAG 2 n E NAG 2 E 2 NAG B 1336 NAG 2 n E BMA 3 E 3 BMA B 1350 BMA 2 n F NAG 1 F 1 NAG B 1337 NAG 2 n F NAG 2 F 2 NAG B 1338 NAG 2 n F BMA 3 F 3 BMA B 1339 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 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 B SG CYS 111 B CYS 110 1_555 B SG CYS 188 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A ND2 ASN 3 A ASN 2 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 A ND2 ASN 16 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale4 A NZ LYS 297 A LYS 296 1_555 G C15 RET . A RET 1332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 A SG CYS 323 A CYS 322 1_555 H C1 PLM . A PLM 1333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.794 ? covale ? covale6 A SG CYS 324 A CYS 323 1_555 I C1 PLM . A PLM 1334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? covale ? covale7 B C ACE 1 B ACE 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 B ND2 ASN 3 B ASN 2 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale9 B ND2 ASN 16 B ASN 15 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 B NZ LYS 297 B LYS 296 1_555 S C15 RET . B RET 1332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale11 B SG CYS 323 B CYS 322 1_555 T C1 PLM . B PLM 1333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.801 ? covale ? covale12 B SG CYS 324 B CYS 323 1_555 U C1 PLM . B PLM 1334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? covale ? covale13 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale14 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale15 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale16 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale17 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale18 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale19 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale20 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? metalc ? metalc1 B ND2 ASN 152 B ASN 151 1_555 EA ZN ZN . B ZN 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? # _chem_comp.formula 'C14 H31 N O' _chem_comp.formula_weight 229.402 _chem_comp.id LDA _chem_comp.mon_nstd_flag . _chem_comp.name 'LAURYL DIMETHYLAMINE-N-OXIDE' _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 N1 O1 LDA sing 257 n n N1 CM1 LDA sing 258 n n N1 CM2 LDA sing 259 n n N1 C1 LDA sing 260 n n CM1 HM11 LDA sing 261 n n CM1 HM12 LDA sing 262 n n CM1 HM13 LDA sing 263 n n CM2 HM21 LDA sing 264 n n CM2 HM22 LDA sing 265 n n CM2 HM23 LDA sing 266 n n C1 C2 LDA sing 267 n n C1 H11 LDA sing 268 n n C1 H12 LDA sing 269 n n C2 C3 LDA sing 270 n n C2 H21 LDA sing 271 n n C2 H22 LDA sing 272 n n C3 C4 LDA sing 273 n n C3 H31 LDA sing 274 n n C3 H32 LDA sing 275 n n C4 C5 LDA sing 276 n n C4 H41 LDA sing 277 n n C4 H42 LDA sing 278 n n C5 C6 LDA sing 279 n n C5 H51 LDA sing 280 n n C5 H52 LDA sing 281 n n C6 C7 LDA sing 282 n n C6 H61 LDA sing 283 n n C6 H62 LDA sing 284 n n C7 C8 LDA sing 285 n n C7 H71 LDA sing 286 n n C7 H72 LDA sing 287 n n C8 C9 LDA sing 288 n n C8 H81 LDA sing 289 n n C8 H82 LDA sing 290 n n C9 C10 LDA sing 291 n n C9 H91 LDA sing 292 n n C9 H92 LDA sing 293 n n C10 C11 LDA sing 294 n n C10 H101 LDA sing 295 n n C10 H102 LDA sing 296 n n C11 C12 LDA sing 297 n n C11 H111 LDA sing 298 n n C11 H112 LDA sing 299 n n C12 H121 LDA sing 300 n n C12 H122 LDA sing 301 n n C12 H123 LDA sing 302 n n # _atom_sites.entry_id 1GZM _atom_sites.fract_transf_matrix[1][1] 0.009632 _atom_sites.fract_transf_matrix[1][2] 0.005561 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011122 _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] 0.013057 _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 G 3 RET A 1 1332 1332 RET RET . H 4 PLM A 1 1333 1333 PLM PLM . I 4 PLM A 1 1334 1334 PLM PLM . J 5 PEF A 1 1341 1341 PEF PEF . K 6 LDA A 1 1342 1342 LDA LDA . L 7 C8E A 1 1343 1343 C8E C8E . M 7 C8E A 1 1344 1344 C8E C8E . N 7 C8E A 1 1345 1345 C8E C8E . O 7 C8E A 1 1346 1346 C8E C8E . P 7 C8E A 1 1347 1347 C8E C8E . Q 7 C8E A 1 1348 1348 C8E C8E . R 8 ZN A 1 1349 1349 ZN ZN . S 3 RET B 1 1332 1332 RET RET . T 4 PLM B 1 1333 1333 PLM PLM . U 4 PLM B 1 1334 1334 PLM PLM . V 7 C8E B 1 1340 1340 C8E C8E . W 7 C8E B 1 1341 1341 C8E C8E . X 5 PEF B 1 1342 1342 PEF PEF . Y 6 LDA B 1 1343 1343 LDA LDA . Z 7 C8E B 1 1344 1344 C8E C8E . AA 7 C8E B 1 1345 1345 C8E C8E . BA 7 C8E B 1 1346 1346 C8E C8E . CA 7 C8E B 1 1347 1347 C8E C8E . DA 6 LDA B 1 1348 1348 LDA LDA . EA 8 ZN B 1 1349 1349 ZN ZN . FA 9 HOH A 1 2001 2001 HOH HOH . FA 9 HOH A 2 2002 2002 HOH HOH . FA 9 HOH A 3 2003 2003 HOH HOH . FA 9 HOH A 4 2004 2004 HOH HOH . FA 9 HOH A 5 2005 2005 HOH HOH . FA 9 HOH A 6 2006 2006 HOH HOH . FA 9 HOH A 7 2007 2007 HOH HOH . FA 9 HOH A 8 2008 2008 HOH HOH . FA 9 HOH A 9 2009 2009 HOH HOH . FA 9 HOH A 10 2010 2010 HOH HOH . FA 9 HOH A 11 2011 2011 HOH HOH . FA 9 HOH A 12 2012 2012 HOH HOH . FA 9 HOH A 13 2013 2013 HOH HOH . FA 9 HOH A 14 2014 2014 HOH HOH . FA 9 HOH A 15 2015 2015 HOH HOH . FA 9 HOH A 16 2016 2016 HOH HOH . FA 9 HOH A 17 2017 2017 HOH HOH . FA 9 HOH A 18 2018 2018 HOH HOH . FA 9 HOH A 19 2019 2019 HOH HOH . FA 9 HOH A 20 2020 2020 HOH HOH . GA 9 HOH B 1 2001 2001 HOH HOH . GA 9 HOH B 2 2002 2002 HOH HOH . GA 9 HOH B 3 2003 2003 HOH HOH . GA 9 HOH B 4 2004 2004 HOH HOH . GA 9 HOH B 5 2005 2005 HOH HOH . GA 9 HOH B 6 2006 2006 HOH HOH . GA 9 HOH B 7 2007 2007 HOH HOH . GA 9 HOH B 8 2008 2008 HOH HOH . GA 9 HOH B 9 2009 2009 HOH HOH . GA 9 HOH B 10 2010 2010 HOH HOH . GA 9 HOH B 11 2011 2011 HOH HOH . GA 9 HOH B 12 2012 2012 HOH HOH . GA 9 HOH B 13 2013 2013 HOH HOH . GA 9 HOH B 14 2014 2014 HOH HOH . GA 9 HOH B 15 2015 2015 HOH HOH . GA 9 HOH B 16 2016 2016 HOH HOH . GA 9 HOH B 17 2017 2017 HOH HOH . GA 9 HOH B 18 2018 2018 HOH HOH . GA 9 HOH B 19 2019 2019 HOH HOH . GA 9 HOH B 20 2020 2020 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 N N1 LDA . . . Y 6 24.643 8.686 9.274 0.5 31.09 ? N1 LDA 1343 B 1 HETATM 2 O O1 LDA . . . Y 6 25.419 9.533 10.097 0.5 33.77 ? O1 LDA 1343 B 1 HETATM 3 C CM1 LDA . . . Y 6 25.546 7.581 8.785 0.5 29.43 ? CM1 LDA 1343 B 1 HETATM 4 C CM2 LDA . . . Y 6 23.498 8.051 10.02 0.5 31.79 ? CM2 LDA 1343 B 1 HETATM 5 C C1 LDA . . . Y 6 23.846 9.333 8.151 0.5 29.5 ? C1 LDA 1343 B 1 HETATM 6 C C2 LDA . . . Y 6 23.983 10.84 8.053 0.5 28.94 ? C2 LDA 1343 B 1 HETATM 7 C C3 LDA . . . Y 6 24.559 11.255 6.7 0.5 29.9 ? C3 LDA 1343 B 1 HETATM 8 C C4 LDA . . . Y 6 23.462 11.541 5.676 0.5 28.74 ? C4 LDA 1343 B 1 HETATM 9 C C5 LDA . . . Y 6 24.038 11.944 4.326 0.5 25.52 ? C5 LDA 1343 B 1 HETATM 10 C C6 LDA . . . Y 6 24.923 10.858 3.745 0.5 24.24 ? C6 LDA 1343 B 1 HETATM 11 C C7 LDA . . . Y 6 24.518 10.522 2.321 0.5 25.03 ? C7 LDA 1343 B 1 HETATM 12 C C8 LDA . . . Y 6 25.517 9.578 1.689 0.5 25.47 ? C8 LDA 1343 B 1 HETATM 13 C C9 LDA . . . Y 6 26.199 10.212 0.495 0.5 25.68 ? C9 LDA 1343 B 1 HETATM 14 C C10 LDA . . . Y 6 25.259 10.317 -0.686 0.5 25.75 ? C10 LDA 1343 B 1 HETATM 15 C C11 LDA . . . Y 6 25.779 9.502 -1.862 0.5 26 ? C11 LDA 1343 B 1 HETATM 16 C C12 LDA . . . Y 6 27.25 9.7 -2.169 0.5 23.73 ? C12 LDA 1343 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 438 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #