data_5J06 # _model_server_result.job_id Z7Dyl2GDMItnu6bC2cWWlg _model_server_result.datetime_utc '2024-11-12 21:13:35' _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 5j06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":304}' # _entry.id 5J06 # _exptl.entry_id 5J06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 5 _entity.src_method syn _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 90 _cell.entry_id 5J06 _cell.length_a 65.05 _cell.length_b 127.06 _cell.length_c 142.83 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5J06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,F,G,H,R,S,T,U,V,Y 1 1 C,N,O,P,Q,X 2 1 B,E,I,J,K,L,M,W 2 2 # 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' 4_445 x-1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 -32.525 -63.53 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id U _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 SIA _pdbx_entity_branch_link.comp_id_2 GAL _pdbx_entity_branch_link.atom_id_1 C2 _pdbx_entity_branch_link.leaving_atom_id_1 O2 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 E GAL 1 E 1 GAL B 8301 GAL 2 n E SIA 2 E 2 SIA B 8300 SIA # 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 19 A CYS 36 1_555 A SG CYS 152 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 24 A CYS 41 1_555 A SG CYS 84 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 146 A CYS 163 1_555 A SG CYS 195 A CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 19 B CYS 36 1_555 B SG CYS 152 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 B SG CYS 24 B CYS 41 1_555 B SG CYS 84 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 B SG CYS 146 B CYS 163 1_555 B SG CYS 195 B CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 C SG CYS 19 C CYS 36 1_555 C SG CYS 152 C CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 C SG CYS 24 C CYS 41 1_555 C SG CYS 84 C CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 146 C CYS 163 1_555 C SG CYS 195 C CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 D SG CYS 19 D CYS 36 1_555 D SG CYS 152 D CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf11 D SG CYS 24 D CYS 41 1_555 D SG CYS 84 D CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 D SG CYS 146 D CYS 163 1_555 D SG CYS 195 D CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 83 A ASN 100 1_555 F C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 143 A ASN 160 1_555 G C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 A ND2 ASN 192 A ASN 209 1_555 H C1 NAG . A NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 B ND2 ASN 83 B ASN 100 1_555 I C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 B ND2 ASN 143 B ASN 160 1_555 J C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 B ND2 ASN 192 B ASN 209 1_555 K C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 B ND2 ASN 213 B ASN 230 1_555 L C1 NAG . B NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale8 C ND2 ASN 83 C ASN 100 1_555 N C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 C ND2 ASN 143 C ASN 160 1_555 O C1 NAG . C NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale10 C ND2 ASN 192 C ASN 209 1_555 P C1 NAG . C NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 D ND2 ASN 83 D ASN 100 1_555 R C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale12 D ND2 ASN 143 D ASN 160 1_555 S C1 NAG . D NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale13 D ND2 ASN 192 D ASN 209 1_555 T C1 NAG . D NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale14 E O3 GAL . E GAL 1 1_555 E C2 SIA . E SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? # _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 363 n n C1 O1A SIA doub 364 n n C1 O1B SIA sing 365 n n C2 C3 SIA sing 366 n n C2 O2 SIA sing 367 n n C2 O6 SIA sing 368 n n C3 C4 SIA sing 369 n n C3 H32 SIA sing 370 n n C3 H31 SIA sing 371 n n C4 C5 SIA sing 372 n n C4 O4 SIA sing 373 n n C4 H4 SIA sing 374 n n C5 C6 SIA sing 375 n n C5 N5 SIA sing 376 n n C5 H5 SIA sing 377 n n C6 C7 SIA sing 378 n n C6 O6 SIA sing 379 n n C6 H6 SIA sing 380 n n C7 C8 SIA sing 381 n n C7 O7 SIA sing 382 n n C7 H7 SIA sing 383 n n C8 C9 SIA sing 384 n n C8 O8 SIA sing 385 n n C8 H8 SIA sing 386 n n C9 O9 SIA sing 387 n n C9 H92 SIA sing 388 n n C9 H91 SIA sing 389 n n C10 C11 SIA sing 390 n n C10 N5 SIA sing 391 n n C10 O10 SIA doub 392 n n C11 H111 SIA sing 393 n n C11 H113 SIA sing 394 n n C11 H112 SIA sing 395 n n N5 HN5 SIA sing 396 n n O1B HO1B SIA sing 397 n n O2 HO2 SIA sing 398 n n O4 HO4 SIA sing 399 n n O7 HO7 SIA sing 400 n n O8 HO8 SIA sing 401 n n O9 HO9 SIA sing 402 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 5J06 _atom_sites.fract_transf_matrix[1][1] 0.015373 _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] 0.00787 _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] 0.007001 _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 F 3 NAG A 1 301 9100 NAG NAG . G 3 NAG A 1 302 9160 NAG NAG . H 3 NAG A 1 303 9209 NAG NAG . I 3 NAG B 1 301 8100 NAG NAG . J 3 NAG B 1 302 8160 NAG NAG . K 3 NAG B 1 303 8209 NAG NAG . L 3 NAG B 1 304 8230 NAG NAG . M 4 PG0 B 1 307 8400 PG0 PG0 . N 3 NAG C 1 301 7100 NAG NAG . O 3 NAG C 1 302 7160 NAG NAG . P 3 NAG C 1 303 7209 NAG NAG . Q 4 PG0 C 1 304 7400 PG0 PG0 . R 3 NAG D 1 301 6100 NAG NAG . S 3 NAG D 1 302 6160 NAG NAG . T 3 NAG D 1 303 6209 NAG NAG . U 5 SIA D 1 304 6300 SIA SIA . V 6 HOH A 1 401 30 HOH HOH . V 6 HOH A 2 402 3 HOH HOH . V 6 HOH A 3 403 39 HOH HOH . V 6 HOH A 4 404 36 HOH HOH . V 6 HOH A 5 405 5 HOH HOH . V 6 HOH A 6 406 48 HOH HOH . V 6 HOH A 7 407 2 HOH HOH . V 6 HOH A 8 408 13 HOH HOH . V 6 HOH A 9 409 6 HOH HOH . V 6 HOH A 10 410 16 HOH HOH . W 6 HOH B 1 401 43 HOH HOH . W 6 HOH B 2 402 8 HOH HOH . W 6 HOH B 3 403 27 HOH HOH . W 6 HOH B 4 404 1 HOH HOH . W 6 HOH B 5 405 15 HOH HOH . W 6 HOH B 6 406 29 HOH HOH . W 6 HOH B 7 407 7 HOH HOH . W 6 HOH B 8 408 9 HOH HOH . W 6 HOH B 9 409 46 HOH HOH . W 6 HOH B 10 410 11 HOH HOH . W 6 HOH B 11 411 21 HOH HOH . W 6 HOH B 12 412 26 HOH HOH . W 6 HOH B 13 413 22 HOH HOH . W 6 HOH B 14 414 25 HOH HOH . X 6 HOH C 1 401 12 HOH HOH . X 6 HOH C 2 402 20 HOH HOH . X 6 HOH C 3 403 32 HOH HOH . X 6 HOH C 4 404 17 HOH HOH . Y 6 HOH D 1 401 33 HOH HOH . Y 6 HOH D 2 402 4 HOH HOH . Y 6 HOH D 3 403 28 HOH HOH . Y 6 HOH D 4 404 23 HOH HOH . Y 6 HOH D 5 405 34 HOH HOH . Y 6 HOH D 6 406 19 HOH HOH . Y 6 HOH D 7 407 44 HOH HOH . Y 6 HOH D 8 408 47 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 . . . U 5 -37.239 3.552 29.582 1 106.95 ? C1 SIA 304 D 1 HETATM 2 C C2 SIA . . . U 5 -37.476 2.334 30.482 1 104.99 ? C2 SIA 304 D 1 HETATM 3 C C3 SIA . . . U 5 -38.195 2.686 31.773 1 96.92 ? C3 SIA 304 D 1 HETATM 4 C C4 SIA . . . U 5 -39.629 3.137 31.51 1 96.33 ? C4 SIA 304 D 1 HETATM 5 C C5 SIA . . . U 5 -40.354 2.091 30.675 1 96.15 ? C5 SIA 304 D 1 HETATM 6 C C6 SIA . . . U 5 -39.578 1.817 29.393 1 99.81 ? C6 SIA 304 D 1 HETATM 7 C C7 SIA . . . U 5 -40.195 0.715 28.535 1 98.1 ? C7 SIA 304 D 1 HETATM 8 C C8 SIA . . . U 5 -39.374 0.37 27.291 1 96.89 ? C8 SIA 304 D 1 HETATM 9 C C9 SIA . . . U 5 -40.232 -0.246 26.2 1 90.75 ? C9 SIA 304 D 1 HETATM 10 C C10 SIA . . . U 5 -42.74 2.315 31.193 1 97.1 ? C10 SIA 304 D 1 HETATM 11 C C11 SIA . . . U 5 -44.063 2.864 30.745 1 93.05 ? C11 SIA 304 D 1 HETATM 12 N N5 SIA . . . U 5 -41.701 2.557 30.386 1 97.42 ? N5 SIA 304 D 1 HETATM 13 O O1A SIA . . . U 5 -37.392 3.316 28.306 1 100.51 ? O1A SIA 304 D 1 HETATM 14 O O1B SIA . . . U 5 -36.924 4.642 30.021 1 111.01 ? O1B SIA 304 D 1 HETATM 15 O O2 SIA . . . U 5 -36.226 1.799 30.776 1 100.95 ? O2 SIA 304 D 1 HETATM 16 O O4 SIA . . . U 5 -40.321 3.334 32.744 1 102.18 ? O4 SIA 304 D 1 HETATM 17 O O6 SIA . . . U 5 -38.238 1.398 29.709 1 105.96 ? O6 SIA 304 D 1 HETATM 18 O O7 SIA . . . U 5 -40.318 -0.46 29.327 1 100.16 ? O7 SIA 304 D 1 HETATM 19 O O8 SIA . . . U 5 -38.751 1.552 26.789 1 98.42 ? O8 SIA 304 D 1 HETATM 20 O O9 SIA . . . U 5 -39.427 -0.814 25.175 1 88.56 ? O9 SIA 304 D 1 HETATM 21 O O10 SIA . . . U 5 -42.618 1.683 32.239 1 90.9 ? O10 SIA 304 D 1 HETATM 22 H H32 SIA . . . U 5 -37.715 3.404 32.216 1 116.3 ? H32 SIA 304 D 1 HETATM 23 H H31 SIA . . . U 5 -38.209 1.906 32.35 1 116.3 ? H31 SIA 304 D 1 HETATM 24 H H4 SIA . . . U 5 -39.61 3.972 31.018 1 115.6 ? H4 SIA 304 D 1 HETATM 25 H H5 SIA . . . U 5 -40.407 1.269 31.186 1 115.38 ? H5 SIA 304 D 1 HETATM 26 H H6 SIA . . . U 5 -39.534 2.636 28.874 1 119.77 ? H6 SIA 304 D 1 HETATM 27 H H7 SIA . . . U 5 -41.08 0.997 28.255 1 117.72 ? H7 SIA 304 D 1 HETATM 28 H H8 SIA . . . U 5 -38.684 -0.265 27.54 1 116.27 ? H8 SIA 304 D 1 HETATM 29 H H92 SIA . . . U 5 -40.798 0.441 25.815 1 108.9 ? H92 SIA 304 D 1 HETATM 30 H H91 SIA . . . U 5 -40.79 -0.938 26.586 1 108.9 ? H91 SIA 304 D 1 HETATM 31 H H111 SIA . . . U 5 -44.436 2.288 30.059 1 111.66 ? H111 SIA 304 D 1 HETATM 32 H H113 SIA . . . U 5 -43.938 3.756 30.386 1 111.66 ? H113 SIA 304 D 1 HETATM 33 H H112 SIA . . . U 5 -44.67 2.901 31.501 1 111.66 ? H112 SIA 304 D 1 HETATM 34 H HN5 SIA . . . U 5 -41.836 3.003 29.664 1 116.91 ? HN5 SIA 304 D 1 HETATM 35 H HO2 SIA . . . U 5 -35.761 1.758 30.065 1 121.15 ? HO2 SIA 304 D 1 HETATM 36 H HO4 SIA . . . U 5 -39.913 3.918 33.207 1 122.62 ? HO4 SIA 304 D 1 HETATM 37 H HO7 SIA . . . U 5 -39.545 -0.759 29.512 1 120.19 ? HO7 SIA 304 D 1 HETATM 38 H HO8 SIA . . . U 5 -39.318 2.184 26.768 1 118.11 ? HO8 SIA 304 D 1 HETATM 39 H HO9 SIA . . . U 5 -39.891 -0.907 24.469 1 106.27 ? HO9 SIA 304 D 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #