data_1LYA # _model_server_result.job_id aprXIbv7noORhHZaXjzOrg _model_server_result.datetime_utc '2024-11-21 16:00:28' _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 1lya # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1}' # _entry.id 1LYA # _exptl.entry_id 1LYA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 1LYA _cell.length_a 125.9 _cell.length_b 125.9 _cell.length_c 104.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1LYA _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L 1 1 A,B,E,G,I,J 2 1 C,D,F,H,K,L 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' 2_664 -y+1,x-y+1,z-1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 62.95 109.032598 -34.7 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 H 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 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . 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 E NAG 1 E 1 NAG A 1 NAG 3 n E NAG 2 E 2 NAG A 2 NAG 3 n E BMA 3 E 3 BMA A 3 MAN 3 n E MAN 4 E 4 MAN A 8 MAN 3 n F NAG 1 F 1 NAG C 1 NAG 3 n F NAG 2 F 2 NAG C 2 NAG 3 n F BMA 3 F 3 BMA C 3 MAN 3 n F MAN 4 F 4 MAN C 8 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 27 A CYS 27 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 46 A CYS 46 1_555 A SG CYS 53 A CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf3 B SG CYS 117 B CYS 222 1_555 B SG CYS 121 B CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 B SG CYS 160 B CYS 265 1_555 B SG CYS 197 B CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf5 C SG CYS 27 C CYS 27 1_555 C SG CYS 96 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf6 C SG CYS 46 C CYS 46 1_555 C SG CYS 53 C CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf7 D SG CYS 117 D CYS 222 1_555 D SG CYS 121 D CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? disulf ? disulf8 D SG CYS 160 D CYS 265 1_555 D SG CYS 197 D CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 70 A ASN 70 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale2 G C1 NAG . B NAG 1 1_555 B ND2 ASN 94 B ASN 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 C ND2 ASN 70 C ASN 70 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 H C1 NAG . D NAG 1 1_555 D ND2 ASN 94 D ASN 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale7 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 1LYA _atom_sites.fract_transf_matrix[1][1] 0.007943 _atom_sites.fract_transf_matrix[1][2] 0.004586 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009172 _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] 0.009606 _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 4 NAG B 1 1 1 NAG NAG . H 4 NAG D 1 1 1 NAG NAG . I 5 HOH A 1 102 1 HOH HOH . I 5 HOH A 2 103 2 HOH HOH . I 5 HOH A 3 104 3 HOH HOH . I 5 HOH A 4 105 4 HOH HOH . I 5 HOH A 5 106 5 HOH HOH . I 5 HOH A 6 107 6 HOH HOH . I 5 HOH A 7 108 9 HOH HOH . I 5 HOH A 8 109 10 HOH HOH . I 5 HOH A 9 110 11 HOH HOH . I 5 HOH A 10 111 28 HOH HOH . I 5 HOH A 11 112 1 HOH HOH . J 5 HOH B 1 33 12 HOH HOH . J 5 HOH B 2 34 13 HOH HOH . J 5 HOH B 3 35 15 HOH HOH . J 5 HOH B 4 36 21 HOH HOH . J 5 HOH B 5 37 22 HOH HOH . J 5 HOH B 6 38 24 HOH HOH . J 5 HOH B 7 39 25 HOH HOH . J 5 HOH B 8 40 26 HOH HOH . J 5 HOH B 9 42 29 HOH HOH . J 5 HOH B 10 43 118 HOH HOH . J 5 HOH B 11 44 120 HOH HOH . J 5 HOH B 12 45 122 HOH HOH . K 5 HOH C 1 102 3 HOH HOH . K 5 HOH C 2 103 4 HOH HOH . K 5 HOH C 3 104 5 HOH HOH . K 5 HOH C 4 105 6 HOH HOH . K 5 HOH C 5 106 9 HOH HOH . K 5 HOH C 6 107 10 HOH HOH . K 5 HOH C 7 108 11 HOH HOH . K 5 HOH C 8 109 28 HOH HOH . L 5 HOH D 1 347 1 HOH HOH . L 5 HOH D 2 348 2 HOH HOH . L 5 HOH D 3 349 12 HOH HOH . L 5 HOH D 4 350 13 HOH HOH . L 5 HOH D 5 351 15 HOH HOH . L 5 HOH D 6 352 21 HOH HOH . L 5 HOH D 7 353 22 HOH HOH . L 5 HOH D 8 354 24 HOH HOH . L 5 HOH D 9 355 25 HOH HOH . L 5 HOH D 10 356 26 HOH HOH . L 5 HOH D 11 357 29 HOH HOH . L 5 HOH D 12 358 118 HOH HOH . L 5 HOH D 13 359 120 HOH HOH . L 5 HOH D 14 360 122 HOH HOH . L 5 HOH D 15 361 1 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 4 3.348 52.677 -13.595 1 78.78 ? C1 NAG 1 D 1 HETATM 2 C C2 NAG . . . H 4 4.626 53.448 -13.986 1 82.9 ? C2 NAG 1 D 1 HETATM 3 C C3 NAG . . . H 4 4.797 53.299 -15.507 1 84.63 ? C3 NAG 1 D 1 HETATM 4 C C4 NAG . . . H 4 4.753 51.803 -15.842 1 84.51 ? C4 NAG 1 D 1 HETATM 5 C C5 NAG . . . H 4 3.317 51.268 -15.64 1 84.07 ? C5 NAG 1 D 1 HETATM 6 C C6 NAG . . . H 4 3.201 49.825 -15.087 1 85.47 ? C6 NAG 1 D 1 HETATM 7 C C7 NAG . . . H 4 4.765 55.208 -12.305 1 87.51 ? C7 NAG 1 D 1 HETATM 8 C C8 NAG . . . H 4 4.582 56.654 -11.883 1 88.98 ? C8 NAG 1 D 1 HETATM 9 N N2 NAG . . . H 4 4.497 54.845 -13.57 1 85.2 ? N2 NAG 1 D 1 HETATM 10 O O3 NAG . . . H 4 6.006 53.884 -15.994 1 85.45 ? O3 NAG 1 D 1 HETATM 11 O O4 NAG . . . H 4 5.174 51.642 -17.178 1 84.98 ? O4 NAG 1 D 1 HETATM 12 O O5 NAG . . . H 4 2.621 52.154 -14.736 1 81.76 ? O5 NAG 1 D 1 HETATM 13 O O6 NAG . . . H 4 4.27 49.468 -14.205 1 86.93 ? O6 NAG 1 D 1 HETATM 14 O O7 NAG . . . H 4 5.191 54.386 -11.489 1 90.36 ? O7 NAG 1 D 1 HETATM 15 H H1 NAG . . . H 4 2.611 53.357 -13.133 1 20 ? H1 NAG 1 D 1 HETATM 16 H H2 NAG . . . H 4 5.502 52.999 -13.492 1 20 ? H2 NAG 1 D 1 HETATM 17 H H3 NAG . . . H 4 3.932 53.778 -15.994 1 20 ? H3 NAG 1 D 1 HETATM 18 H H4 NAG . . . H 4 5.444 51.274 -15.17 1 20 ? H4 NAG 1 D 1 HETATM 19 H H5 NAG . . . H 4 2.757 51.327 -16.586 1 20 ? H5 NAG 1 D 1 HETATM 20 H H61 NAG . . . H 4 3.151 49.133 -15.943 1 20 ? H61 NAG 1 D 1 HETATM 21 H H62 NAG . . . H 4 2.239 49.74 -14.554 1 20 ? H62 NAG 1 D 1 HETATM 22 H H81 NAG . . . H 4 3.864 57.165 -12.537 1 20 ? H81 NAG 1 D 1 HETATM 23 H H82 NAG . . . H 4 5.546 57.181 -11.911 1 20 ? H82 NAG 1 D 1 HETATM 24 H H83 NAG . . . H 4 4.201 56.698 -10.851 1 20 ? H83 NAG 1 D 1 HETATM 25 H HN2 NAG . . . H 4 4.187 55.511 -14.214 1 20 ? HN2 NAG 1 D 1 HETATM 26 H HO3 NAG . . . H 4 6.083 54.787 -15.68 1 20 ? HO3 NAG 1 D 1 HETATM 27 H HO4 NAG . . . H 4 5.862 52.31 -17.308 1 20 ? HO4 NAG 1 D 1 HETATM 28 H HO6 NAG . . . H 4 4.873 48.886 -14.683 1 20 ? HO6 NAG 1 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 962 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #