data_5VJL # _model_server_result.job_id sak-A8Qql4VsDUJNhZHLsA _model_server_result.datetime_utc '2024-11-24 09:30:32' _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 5vjl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":3001}' # _entry.id 5VJL # _exptl.entry_id 5VJL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'N-acetyl-alpha-neuraminic acid' _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 120 _cell.entry_id 5VJL _cell.length_a 116.375 _cell.length_b 116.375 _cell.length_c 296.008 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VJL _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -58.1875 100.783706 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -116.375 0 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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 272 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 133 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf5 A SG CYS 276 A CYS 281 1_555 A SG CYS 300 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? covale ? covale1 A ND2 ASN 32 A ASN 38 1_555 F C1 NAG . A NAG 3004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale2 A ND2 ASN 235 A ASN 240 1_555 E C1 NAG . A NAG 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C C2 SIA . A SIA 3001 1_555 D O MOH . A MOH 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 B ND2 ASN 82 B ASN 82 1_555 G C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.536 ? # _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 'N-acetylneuraminic acid;sialic acid;alpha-sialic acid;O-SIALIC ACID' # 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 C2 SIA sing 325 n n C1 O1A SIA doub 326 n n C1 O1B SIA sing 327 n n C2 C3 SIA sing 328 n n C2 O2 SIA sing 329 n n C2 O6 SIA sing 330 n n C3 C4 SIA sing 331 n n C3 H32 SIA sing 332 n n C3 H31 SIA sing 333 n n C4 C5 SIA sing 334 n n C4 O4 SIA sing 335 n n C4 H4 SIA sing 336 n n C5 C6 SIA sing 337 n n C5 N5 SIA sing 338 n n C5 H5 SIA sing 339 n n C6 C7 SIA sing 340 n n C6 O6 SIA sing 341 n n C6 H6 SIA sing 342 n n C7 C8 SIA sing 343 n n C7 O7 SIA sing 344 n n C7 H7 SIA sing 345 n n C8 C9 SIA sing 346 n n C8 O8 SIA sing 347 n n C8 H8 SIA sing 348 n n C9 O9 SIA sing 349 n n C9 H92 SIA sing 350 n n C9 H91 SIA sing 351 n n C10 C11 SIA sing 352 n n C10 N5 SIA sing 353 n n C10 O10 SIA doub 354 n n C11 H111 SIA sing 355 n n C11 H113 SIA sing 356 n n C11 H112 SIA sing 357 n n N5 HN5 SIA sing 358 n n O1B HO1B SIA sing 359 n n O2 HO2 SIA sing 360 n n O4 HO4 SIA sing 361 n n O7 HO7 SIA sing 362 n n O8 HO8 SIA sing 363 n n O9 HO9 SIA sing 364 n n # 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 5VJL _atom_sites.fract_transf_matrix[1][1] 0.008593 _atom_sites.fract_transf_matrix[1][2] 0.004961 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009922 _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] 0.003378 _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 SIA A 1 3001 3001 SIA SIA . D 4 MOH A 1 3002 3002 MOH GAL . E 5 NAG A 1 3003 501 NAG NAG . F 5 NAG A 1 3004 502 NAG NAG . G 5 NAG B 1 201 502 NAG NAG . H 6 HOH A 1 3101 2 HOH HOH . H 6 HOH A 2 3102 16 HOH HOH . H 6 HOH A 3 3103 15 HOH HOH . H 6 HOH A 4 3104 8 HOH HOH . H 6 HOH A 5 3105 9 HOH HOH . H 6 HOH A 6 3106 3 HOH HOH . H 6 HOH A 7 3107 20 HOH HOH . H 6 HOH A 8 3108 21 HOH HOH . H 6 HOH A 9 3109 31 HOH HOH . H 6 HOH A 10 3110 17 HOH HOH . H 6 HOH A 11 3111 11 HOH HOH . H 6 HOH A 12 3112 30 HOH HOH . H 6 HOH A 13 3113 19 HOH HOH . H 6 HOH A 14 3114 18 HOH HOH . I 6 HOH B 1 301 4 HOH HOH . I 6 HOH B 2 302 10 HOH HOH . I 6 HOH B 3 303 1 HOH HOH . I 6 HOH B 4 304 14 HOH HOH . I 6 HOH B 5 305 6 HOH HOH . I 6 HOH B 6 306 5 HOH HOH . I 6 HOH B 7 307 23 HOH HOH . I 6 HOH B 8 308 12 HOH HOH . I 6 HOH B 9 309 7 HOH HOH . I 6 HOH B 10 310 22 HOH HOH . I 6 HOH B 11 311 26 HOH HOH . I 6 HOH B 12 312 13 HOH HOH . I 6 HOH B 13 313 27 HOH HOH . I 6 HOH B 14 314 24 HOH HOH . I 6 HOH B 15 315 28 HOH HOH . I 6 HOH B 16 316 25 HOH HOH . I 6 HOH B 17 317 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 . . . C 3 -44.281 9.942 -35.62 1 147.63 ? C1 SIA 3001 A 1 HETATM 2 C C2 SIA . . . C 3 -44.159 10.372 -37.139 1 131.76 ? C2 SIA 3001 A 1 HETATM 3 C C3 SIA . . . C 3 -44.742 9.242 -38 1 122.75 ? C3 SIA 3001 A 1 HETATM 4 C C4 SIA . . . C 3 -46.224 9.031 -37.687 1 108.43 ? C4 SIA 3001 A 1 HETATM 5 C C5 SIA . . . C 3 -46.986 10.289 -38.127 1 106.81 ? C5 SIA 3001 A 1 HETATM 6 C C6 SIA . . . C 3 -46.421 11.51 -37.334 1 112.1 ? C6 SIA 3001 A 1 HETATM 7 C C7 SIA . . . C 3 -46.938 12.899 -37.825 1 111.69 ? C7 SIA 3001 A 1 HETATM 8 C C8 SIA . . . C 3 -46.477 14.107 -36.963 1 109.74 ? C8 SIA 3001 A 1 HETATM 9 C C9 SIA . . . C 3 -47.315 15.358 -37.246 1 102.62 ? C9 SIA 3001 A 1 HETATM 10 C C10 SIA . . . C 3 -49.455 10.704 -38.544 1 93.07 ? C10 SIA 3001 A 1 HETATM 11 C C11 SIA . . . C 3 -50.845 10.254 -38.137 1 88.98 ? C11 SIA 3001 A 1 HETATM 12 N N5 SIA . . . C 3 -48.42 10.075 -37.926 1 100.06 ? N5 SIA 3001 A 1 HETATM 13 O O1A SIA . . . C 3 -43.991 8.75 -35.356 1 149.12 ? O1A SIA 3001 A 1 HETATM 14 O O1B SIA . . . C 3 -44.668 10.872 -34.861 1 148.8 ? O1B SIA 3001 A 1 HETATM 15 O O4 SIA . . . C 3 -46.806 7.843 -38.267 1 99.48 ? O4 SIA 3001 A 1 HETATM 16 O O6 SIA . . . C 3 -44.986 11.575 -37.4 1 122.86 ? O6 SIA 3001 A 1 HETATM 17 O O7 SIA . . . C 3 -46.571 13.109 -39.177 1 112.94 ? O7 SIA 3001 A 1 HETATM 18 O O8 SIA . . . C 3 -46.48 13.771 -35.574 1 112.63 ? O8 SIA 3001 A 1 HETATM 19 O O9 SIA . . . C 3 -46.852 16.465 -36.457 1 95.99 ? O9 SIA 3001 A 1 HETATM 20 O O10 SIA . . . C 3 -49.354 11.591 -39.376 1 101.38 ? O10 SIA 3001 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 528 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #