data_5IGX # _model_server_result.job_id 5W_qTyrmWN5yfdVWl4-bDQ _model_server_result.datetime_utc '2024-11-08 14:37:02' _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 5igx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":602}' # _entry.id 5IGX # _exptl.entry_id 5IGX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 5IGX _cell.length_a 146.284 _cell.length_b 168.533 _cell.length_c 176.69 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IGX _symmetry.cell_setting ? _symmetry.Int_Tables_number 22 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'F 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G N N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 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 4 n D NAG 1 A 1 NAG G 496 NAG 4 n D NAG 2 A 2 NAG G 497 NAG 4 n D BMA 3 A 3 BMA G 498 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 11 G CYS 54 1_555 A SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 22 G CYS 65 1_555 A SG CYS 72 G CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf3 A SG CYS 76 G CYS 119 1_555 A SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf4 A SG CYS 102 G CYS 218 1_555 A SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 112 G CYS 228 1_555 A SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 180 G CYS 296 1_555 A SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 A SG CYS 245 G CYS 377 1_555 A SG CYS 298 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf8 A SG CYS 252 G CYS 384 1_555 A SG CYS 271 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf10 B SG CYS 152 H CYS 144 1_555 B SG CYS 208 H CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 C SG CYS 23 L CYS 23 1_555 C SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 C SG CYS 130 L CYS 130 1_555 C SG CYS 190 L CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 81 G ASN 124 1_555 G C1 NAG . G NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 A ND2 ASN 146 G ASN 262 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 173 G ASN 289 1_555 E C1 NAG . G NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale4 A ND2 ASN 253 G ASN 385 1_555 F C1 NAG . G NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 D O4 NAG . A NAG 2 1_555 D C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5IGX _atom_sites.fract_transf_matrix[1][1] 0.006836 _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] 0.005934 _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] 0.00566 _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 E 5 NAG G 1 601 492 NAG NAG . F 5 NAG G 1 602 493 NAG NAG . G 5 NAG G 1 603 495 NAG NAG . # 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 NAG . . . F 5 -67.006 33.713 -7.15 0.99 91.12 ? C1 NAG 602 G 1 HETATM 2 C C2 NAG . . . F 5 -67.963 32.711 -7.818 0.99 85.71 ? C2 NAG 602 G 1 HETATM 3 C C3 NAG . . . F 5 -68.607 33.328 -9.061 0.99 134.94 ? C3 NAG 602 G 1 HETATM 4 C C4 NAG . . . F 5 -69.239 34.673 -8.736 0.99 138.31 ? C4 NAG 602 G 1 HETATM 5 C C5 NAG . . . F 5 -68.198 35.583 -8.103 0.99 82.27 ? C5 NAG 602 G 1 HETATM 6 C C6 NAG . . . F 5 -68.758 36.92 -7.676 0.99 99.45 ? C6 NAG 602 G 1 HETATM 7 C C7 NAG . . . F 5 -67.366 30.345 -7.486 0.99 97.78 ? C7 NAG 602 G 1 HETATM 8 C C8 NAG . . . F 5 -66.569 29.188 -8.012 0.99 108.84 ? C8 NAG 602 G 1 HETATM 9 N N2 NAG . . . F 5 -67.26 31.488 -8.173 0.99 76.84 ? N2 NAG 602 G 1 HETATM 10 O O3 NAG . . . F 5 -69.593 32.438 -9.574 0.99 138.38 ? O3 NAG 602 G 1 HETATM 11 O O4 NAG . . . F 5 -69.748 35.283 -9.917 0.99 165.41 ? O4 NAG 602 G 1 HETATM 12 O O5 NAG . . . F 5 -67.686 34.956 -6.921 0.99 73.58 ? O5 NAG 602 G 1 HETATM 13 O O6 NAG . . . F 5 -68.372 37.24 -6.347 0.99 121.06 ? O6 NAG 602 G 1 HETATM 14 O O7 NAG . . . F 5 -68.068 30.249 -6.488 0.99 118.87 ? O7 NAG 602 G 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #