data_4YY7 # _model_server_result.job_id hudxc9dhVsrp_asU4brduA _model_server_result.datetime_utc '2024-10-19 21:31:10' _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 4yy7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 4YY7 # _exptl.entry_id 4YY7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _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 4YY7 _cell.length_a 96.772 _cell.length_b 96.772 _cell.length_c 132.506 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YY7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_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,E,F,I,J 1 1,2,4 C,D,G,H,K,L 2 1,3,5 # 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_765 -y+2,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 145.158 83.80701 0 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 96.772 0 0 4 'crystal symmetry operation' 3_675 -x+y+1,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 167.614021 0 5 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 48.386 83.80701 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 I N N ? 5 J N N ? 5 K N N ? 5 L 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 GAL NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 SIA GAL C2 O2 . 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 E NAG 1 E 1 NAG A 401 NAG 3 n E NAG 2 E 2 NAG A 402 NAG 4 n F NAG 1 F 1 NAG A 404 NAG 4 n F GAL 2 F 2 GAL A 405 GAL 4 n F SIA 3 F 3 SIA A 403 SIA 3 n G NAG 1 G 1 NAG C 602 NAG 3 n G NAG 2 G 2 NAG C 603 NAG 4 n H NAG 1 H 1 NAG C 803 NAG 4 n H GAL 2 H 2 GAL C 802 GAL 4 n H SIA 3 H 3 SIA C 801 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 4 A CYS 4 1_555 B SG CYS 137 B CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 42 A CYS 42 1_555 A SG CYS 277 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 55 A CYS 55 1_555 A SG CYS 67 A CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 A SG CYS 90 A CYS 90 1_555 A SG CYS 135 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 A SG CYS 281 A CYS 281 1_555 A SG CYS 305 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 144 B CYS 473 1_555 B SG CYS 148 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 C SG CYS 4 C CYS 4 1_555 D SG CYS 137 D CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 C SG CYS 42 C CYS 42 1_555 C SG CYS 277 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 C SG CYS 55 C CYS 55 1_555 C SG CYS 67 C CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf10 C SG CYS 90 C CYS 90 1_555 C SG CYS 135 C CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 C SG CYS 281 C CYS 281 1_555 C SG CYS 305 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf12 D SG CYS 144 D CYS 473 1_555 D SG CYS 148 D CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 23 A ASN 23 1_555 I C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 167 A ASN 167 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B ND2 ASN 154 B ASN 483 1_555 J C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 C ND2 ASN 23 C ASN 23 1_555 K C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 C ND2 ASN 167 C ASN 167 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 D ND2 ASN 154 D ASN 483 1_555 L C1 NAG . D NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 GAL . F GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale9 F O3 GAL . F GAL 2 1_555 F C2 SIA . F SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale10 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale11 H O4 NAG . H NAG 1 1_555 H C1 GAL . H GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale12 H O3 GAL . H GAL 2 1_555 H C2 SIA . H SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? # _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 ? # 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 4YY7 _atom_sites.fract_transf_matrix[1][1] 0.010334 _atom_sites.fract_transf_matrix[1][2] 0.005966 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011932 _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] 0.007547 _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 I 5 NAG A 1 401 326 NAG NAG . J 5 NAG B 1 501 604 NAG NAG . K 5 NAG C 1 601 601 NAG NAG . L 5 NAG D 1 501 604 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 . . . J 5 74.808 86.9 -62.206 1 156.29 ? C1 NAG 501 B 1 HETATM 2 C C2 NAG . . . J 5 75.665 88.08 -61.666 1 154.86 ? C2 NAG 501 B 1 HETATM 3 C C3 NAG . . . J 5 76.844 88.344 -62.588 1 152.47 ? C3 NAG 501 B 1 HETATM 4 C C4 NAG . . . J 5 77.723 87.108 -62.617 1 153.26 ? C4 NAG 501 B 1 HETATM 5 C C5 NAG . . . J 5 76.956 86.008 -63.34 1 155.77 ? C5 NAG 501 B 1 HETATM 6 C C6 NAG . . . J 5 77.753 84.719 -63.424 1 154.37 ? C6 NAG 501 B 1 HETATM 7 C C7 NAG . . . J 5 73.949 89.443 -60.522 1 157.74 ? C7 NAG 501 B 1 HETATM 8 C C8 NAG . . . J 5 73.229 90.78 -60.487 1 150.82 ? C8 NAG 501 B 1 HETATM 9 N N2 NAG . . . J 5 74.877 89.295 -61.485 1 157.55 ? N2 NAG 501 B 1 HETATM 10 O O3 NAG . . . J 5 77.595 89.481 -62.168 1 148.86 ? O3 NAG 501 B 1 HETATM 11 O O4 NAG . . . J 5 78.968 87.398 -63.247 1 152.32 ? O4 NAG 501 B 1 HETATM 12 O O5 NAG . . . J 5 75.738 85.714 -62.621 1 156.75 ? O5 NAG 501 B 1 HETATM 13 O O6 NAG . . . J 5 77.098 83.72 -64.205 1 153.92 ? O6 NAG 501 B 1 HETATM 14 O O7 NAG . . . J 5 73.689 88.531 -59.707 1 158.12 ? O7 NAG 501 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #