data_5HMG # _model_server_result.job_id tt2VBf32olgW7CFAeS_OrQ _model_server_result.datetime_utc '2024-11-07 10:07:23' _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 5hmg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":329}' # _entry.id 5HMG # _exptl.entry_id 5HMG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'N-acetyl-alpha-neuraminic acid' _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 90 _cell.entry_id 5HMG _cell.length_a 162.6 _cell.length_b 162.6 _cell.length_c 177.4 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HMG _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,Z,AA,BA,CA,DA _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 ? 4 J N N ? 4 O N N ? 4 T N N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN 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 3 n G NAG 1 G 1 NAG A 339 NAG 3 n G NAG 2 G 2 NAG A 340 NAG 3 n G MAN 3 G 3 MAN A 341 MAN 3 n H NAG 1 H 1 NAG C 339 NAG 3 n H NAG 2 H 2 NAG C 340 NAG 3 n H MAN 3 H 3 MAN C 341 MAN 3 n I NAG 1 I 1 NAG E 339 NAG 3 n I NAG 2 I 2 NAG E 340 NAG 3 n I MAN 3 I 3 MAN E 341 MAN # 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 14 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf2 A SG CYS 52 A CYS 52 1_555 A SG CYS 277 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 76 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? disulf ? disulf4 A SG CYS 97 A CYS 97 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf5 A SG CYS 281 A CYS 281 1_555 A SG CYS 305 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf7 C SG CYS 14 C CYS 14 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf8 C SG CYS 52 C CYS 52 1_555 C SG CYS 277 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf9 C SG CYS 64 C CYS 64 1_555 C SG CYS 76 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf10 C SG CYS 97 C CYS 97 1_555 C SG CYS 139 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf11 C SG CYS 281 C CYS 281 1_555 C SG CYS 305 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf13 E SG CYS 14 E CYS 14 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf14 E SG CYS 52 E CYS 52 1_555 E SG CYS 277 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf15 E SG CYS 64 E CYS 64 1_555 E SG CYS 76 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? disulf ? disulf16 E SG CYS 97 E CYS 97 1_555 E SG CYS 139 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf17 E SG CYS 281 E CYS 281 1_555 E SG CYS 305 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? covale ? covale1 A ND2 ASN 38 A ASN 38 1_555 K C1 NAG . A NAG 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 81 A ASN 81 1_555 L C1 NAG . A NAG 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale4 A ND2 ASN 285 A ASN 285 1_555 M C1 NAG . A NAG 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 B ND2 ASN 154 B ASN 154 1_555 N C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale6 C ND2 ASN 38 C ASN 38 1_555 P C1 NAG . C NAG 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 C ND2 ASN 81 C ASN 81 1_555 Q C1 NAG . C NAG 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale8 C ND2 ASN 165 C ASN 165 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale9 C ND2 ASN 285 C ASN 285 1_555 R C1 NAG . C NAG 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 D ND2 ASN 154 D ASN 154 1_555 S C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale11 E ND2 ASN 38 E ASN 38 1_555 U C1 NAG . E NAG 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale12 E ND2 ASN 81 E ASN 81 1_555 V C1 NAG . E NAG 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale13 E ND2 ASN 165 E ASN 165 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale14 E ND2 ASN 285 E ASN 285 1_555 W C1 NAG . E NAG 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale15 F ND2 ASN 154 F ASN 154 1_555 X C1 NAG . F NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale16 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale17 G O4 NAG . G NAG 2 1_555 G C1 MAN . G MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale19 H O4 NAG . H NAG 2 1_555 H C1 MAN . H MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale20 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale21 I O4 NAG . I NAG 2 1_555 I C1 MAN . I MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? # _chem_comp.formula 'C11 H19 N O9' _chem_comp.formula_weight 309.27 _chem_comp.id SIA _chem_comp.mon_nstd_flag . _chem_comp.name 'N-acetyl-alpha-neuraminic acid' _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms ? # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version SIA DNeup5Aca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 SIA 'N-acetyl-a-D-neuraminic acid' 'COMMON NAME' GMML 1 SIA a-D-Neup5Ac 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 SIA Neu5Ac 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5HMG _atom_sites.fract_transf_matrix[1][1] 0.00615 _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] 0.00615 _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] 0.005637 _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 J 4 SIA A 1 329 1 SIA SIA . K 5 NAG A 1 330 329 NAG NAG . L 5 NAG A 1 334 334 NAG NAG . M 5 NAG A 1 348 348 NAG NAG . N 5 NAG B 1 401 401 NAG NAG . O 4 SIA C 1 329 1 SIA SIA . P 5 NAG C 1 330 329 NAG NAG . Q 5 NAG C 1 334 334 NAG NAG . R 5 NAG C 1 348 348 NAG NAG . S 5 NAG D 1 401 401 NAG NAG . T 4 SIA E 1 329 1 SIA SIA . U 5 NAG E 1 330 329 NAG NAG . V 5 NAG E 1 334 334 NAG NAG . W 5 NAG E 1 348 348 NAG NAG . X 5 NAG F 1 401 401 NAG NAG . Y 6 HOH A 1 349 2 HOH HOH . Y 6 HOH A 2 350 3 HOH HOH . Y 6 HOH A 3 351 4 HOH HOH . Y 6 HOH A 4 352 5 HOH HOH . Y 6 HOH A 5 353 6 HOH HOH . Y 6 HOH A 6 354 11 HOH HOH . Y 6 HOH A 7 355 12 HOH HOH . Y 6 HOH A 8 356 24 HOH HOH . Z 6 HOH B 1 402 21 HOH HOH . Z 6 HOH B 2 403 22 HOH HOH . Z 6 HOH B 3 404 23 HOH HOH . Z 6 HOH B 4 405 27 HOH HOH . Z 6 HOH B 5 406 29 HOH HOH . AA 6 HOH C 1 349 2 HOH HOH . AA 6 HOH C 2 350 3 HOH HOH . AA 6 HOH C 3 351 4 HOH HOH . AA 6 HOH C 4 352 5 HOH HOH . AA 6 HOH C 5 353 6 HOH HOH . AA 6 HOH C 6 354 11 HOH HOH . AA 6 HOH C 7 355 12 HOH HOH . AA 6 HOH C 8 356 24 HOH HOH . BA 6 HOH D 1 402 21 HOH HOH . BA 6 HOH D 2 403 22 HOH HOH . BA 6 HOH D 3 404 23 HOH HOH . BA 6 HOH D 4 405 27 HOH HOH . BA 6 HOH D 5 406 29 HOH HOH . CA 6 HOH E 1 349 2 HOH HOH . CA 6 HOH E 2 350 3 HOH HOH . CA 6 HOH E 3 351 4 HOH HOH . CA 6 HOH E 4 352 5 HOH HOH . CA 6 HOH E 5 353 6 HOH HOH . CA 6 HOH E 6 354 11 HOH HOH . CA 6 HOH E 7 355 12 HOH HOH . CA 6 HOH E 8 356 23 HOH HOH . CA 6 HOH E 9 357 24 HOH HOH . DA 6 HOH F 1 402 21 HOH HOH . DA 6 HOH F 2 403 22 HOH HOH . DA 6 HOH F 3 404 27 HOH HOH . DA 6 HOH F 4 405 29 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 SIA . . . O 4 -6.657 62.388 -17.125 0.3 49.78 ? C1 SIA 329 C 1 HETATM 2 C C2 SIA . . . O 4 -7.522 63.67 -17.082 0.3 49.9 ? C2 SIA 329 C 1 HETATM 3 C C3 SIA . . . O 4 -9.035 63.299 -16.926 0.3 50.2 ? C3 SIA 329 C 1 HETATM 4 C C4 SIA . . . O 4 -9.442 62.914 -15.505 0.3 50.46 ? C4 SIA 329 C 1 HETATM 5 C C5 SIA . . . O 4 -8.946 63.981 -14.518 0.3 50.26 ? C5 SIA 329 C 1 HETATM 6 C C6 SIA . . . O 4 -7.431 64.146 -14.646 0.3 50.14 ? C6 SIA 329 C 1 HETATM 7 C C7 SIA . . . O 4 -6.791 65.208 -13.76 0.3 50.21 ? C7 SIA 329 C 1 HETATM 8 C C8 SIA . . . O 4 -5.248 65.147 -13.953 0.3 50.31 ? C8 SIA 329 C 1 HETATM 9 C C9 SIA . . . O 4 -4.512 66.009 -12.975 0.3 50.31 ? C9 SIA 329 C 1 HETATM 10 C C10 SIA . . . O 4 -9.996 64.131 -12.298 0.3 49.86 ? C10 SIA 329 C 1 HETATM 11 C C11 SIA . . . O 4 -10.182 63.564 -10.911 0.3 49.83 ? C11 SIA 329 C 1 HETATM 12 N N5 SIA . . . O 4 -9.234 63.494 -13.18 0.3 50.01 ? N5 SIA 329 C 1 HETATM 13 O O1A SIA . . . O 4 -6.397 61.753 -16.128 0.3 49.59 ? O1A SIA 329 C 1 HETATM 14 O O1B SIA . . . O 4 -6.23 61.992 -18.203 0.3 49.83 ? O1B SIA 329 C 1 HETATM 15 O O2 SIA . . . O 4 -7.291 64.377 -18.265 0.3 49.9 ? O2 SIA 329 C 1 HETATM 16 O O4 SIA . . . O 4 -10.85 62.733 -15.333 0.3 50.55 ? O4 SIA 329 C 1 HETATM 17 O O6 SIA . . . O 4 -7.1 64.508 -16.009 0.3 49.98 ? O6 SIA 329 C 1 HETATM 18 O O7 SIA . . . O 4 -7.308 66.459 -14.157 0.3 50.3 ? O7 SIA 329 C 1 HETATM 19 O O8 SIA . . . O 4 -4.683 63.864 -13.831 0.3 50.23 ? O8 SIA 329 C 1 HETATM 20 O O9 SIA . . . O 4 -3.123 65.875 -13.223 0.3 50.5 ? O9 SIA 329 C 1 HETATM 21 O O10 SIA . . . O 4 -10.549 65.176 -12.607 0.3 49.95 ? O10 SIA 329 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #