data_5IYV # _model_server_result.job_id jfyOmuOEJrzIBlO8MeBxKw _model_server_result.datetime_utc '2024-11-15 23:34:38' _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 5iyv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":706}' # _entry.id 5IYV # _exptl.entry_id 5IYV _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 120 _cell.entry_id 5IYV _cell.length_a 150.181 _cell.length_b 150.181 _cell.length_c 60.07 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IYV _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 G N N ? 5 H N N ? 5 I N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . 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 C NAG 1 C 1 NAG A 1098 NAG 3 n C NAG 2 C 2 NAG A 1099 NAG 3 n D NAG 1 D 1 NAG A 1150 NAG 3 n D NAG 2 D 2 NAG A 1151 NAG 4 n E NAG 1 E 1 NAG A 1269 NAG 4 n E NAG 2 E 2 NAG A 1270 NAG 4 n E BMA 3 E 3 BMA A 1271 BMA 4 n E MAN 4 E 4 MAN A 1272 MAN 3 n F NAG 1 F 1 NAG A 1576 NAG 3 n F NAG 2 F 2 NAG A 1577 NAG # 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 40 A CYS 54 1_555 A SG CYS 47 A CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf2 A SG CYS 72 A CYS 86 1_555 A SG CYS 99 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf3 A SG CYS 362 A CYS 376 1_555 A SG CYS 388 A CYS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? covale ? covale1 A ND2 ASN 84 A ASN 98 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 88 A ASN 102 1_555 G C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 A ND2 ASN 136 A ASN 150 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 171 A ASN 185 1_555 H C1 NAG . A NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 255 A ASN 269 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 A ND2 ASN 268 A ASN 282 1_555 I C1 NAG . A NAG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale7 A ND2 ASN 562 A ASN 576 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 B C GLY 6 B GLY 72 1_555 B N HYP 7 B HYP 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale9 B C HYP 7 B HYP 73 1_555 B N SER 8 B SER 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale10 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale13 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale14 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale15 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 312 n n C1 O1 NAG sing 313 n n C1 O5 NAG sing 314 n n C1 H1 NAG sing 315 n n C2 C3 NAG sing 316 n n C2 N2 NAG sing 317 n n C2 H2 NAG sing 318 n n C3 C4 NAG sing 319 n n C3 O3 NAG sing 320 n n C3 H3 NAG sing 321 n n C4 C5 NAG sing 322 n n C4 O4 NAG sing 323 n n C4 H4 NAG sing 324 n n C5 C6 NAG sing 325 n n C5 O5 NAG sing 326 n n C5 H5 NAG sing 327 n n C6 O6 NAG sing 328 n n C6 H61 NAG sing 329 n n C6 H62 NAG sing 330 n n C7 C8 NAG sing 331 n n C7 N2 NAG sing 332 n n C7 O7 NAG doub 333 n n C8 H81 NAG sing 334 n n C8 H82 NAG sing 335 n n C8 H83 NAG sing 336 n n N2 HN2 NAG sing 337 n n O1 HO1 NAG sing 338 n n O3 HO3 NAG sing 339 n n O4 HO4 NAG sing 340 n n O6 HO6 NAG sing 341 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 5IYV _atom_sites.fract_transf_matrix[1][1] 0.006659 _atom_sites.fract_transf_matrix[1][2] 0.003844 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007689 _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] 0.016647 _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 5 NAG A 1 703 1102 NAG NAG . H 5 NAG A 1 706 1185 NAG NAG . I 5 NAG A 1 711 1282 NAG NAG . J 6 EDO B 1 2000 2000 EDO EDO . K 7 HOH A 1 801 3 HOH HOH . K 7 HOH A 2 802 6 HOH HOH . K 7 HOH A 3 803 4 HOH HOH . K 7 HOH A 4 804 7 HOH HOH . K 7 HOH A 5 805 2 HOH HOH . K 7 HOH A 6 806 8 HOH HOH . K 7 HOH A 7 807 1 HOH HOH . K 7 HOH A 8 808 5 HOH HOH . K 7 HOH A 9 809 9 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 NAG . . . H 5 23.467 67.299 -20.936 1 137.8 ? C1 NAG 706 A 1 HETATM 2 C C2 NAG . . . H 5 24.631 67.946 -21.698 1 143.13 ? C2 NAG 706 A 1 HETATM 3 C C3 NAG . . . H 5 25.134 67.02 -22.792 1 140.7 ? C3 NAG 706 A 1 HETATM 4 C C4 NAG . . . H 5 25.339 65.596 -22.27 1 136.94 ? C4 NAG 706 A 1 HETATM 5 C C5 NAG . . . H 5 24.081 65.119 -21.546 1 132 ? C5 NAG 706 A 1 HETATM 6 C C6 NAG . . . H 5 24.2 63.68 -21.053 1 122.96 ? C6 NAG 706 A 1 HETATM 7 C C7 NAG . . . H 5 24.449 70.389 -21.712 1 148.21 ? C7 NAG 706 A 1 HETATM 8 C C8 NAG . . . H 5 23.98 71.595 -22.477 1 143.26 ? C8 NAG 706 A 1 HETATM 9 N N2 NAG . . . H 5 24.243 69.215 -22.305 1 146.87 ? N2 NAG 706 A 1 HETATM 10 O O3 NAG . . . H 5 26.358 67.542 -23.326 1 140.17 ? O3 NAG 706 A 1 HETATM 11 O O4 NAG . . . H 5 25.642 64.727 -23.367 1 134.66 ? O4 NAG 706 A 1 HETATM 12 O O5 NAG . . . H 5 23.825 66.012 -20.456 1 134.83 ? O5 NAG 706 A 1 HETATM 13 O O6 NAG . . . H 5 24.149 63.667 -19.629 1 119.54 ? O6 NAG 706 A 1 HETATM 14 O O7 NAG . . . H 5 24.967 70.463 -20.607 1 145.58 ? O7 NAG 706 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #