data_5T89 # _model_server_result.job_id 2RR3FnhPirBF1VfrWY-dUQ _model_server_result.datetime_utc '2025-04-28 03:32:23' _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 5t89 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":705}' # _entry.id 5T89 # _exptl.entry_id 5T89 _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 19 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.56 _cell.angle_gamma 90 _cell.entry_id 5T89 _cell.length_a 166.71 _cell.length_b 123.09 _cell.length_c 167.37 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5T89 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y _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 ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N ? 4 R N N ? 4 S N N ? 4 T N N ? 4 U N N ? 4 V N N ? 4 W N N ? 4 X N N ? 4 Y N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _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 3 n E NAG 1 A 1 NAG X 700 NAG 3 n E NAG 2 A 2 NAG X 800 NAG 3 n F NAG 1 B 1 NAG Y 702 NAG 3 n F NAG 2 B 2 NAG Y 800 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 36 V CYS 26 1_555 A SG CYS 78 V CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 61 V CYS 51 1_555 B SG CYS 70 W CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 67 V CYS 57 1_555 A SG CYS 112 V CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 70 V CYS 60 1_555 B SG CYS 61 W CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 71 V CYS 61 1_555 A SG CYS 114 V CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 36 W CYS 26 1_555 B SG CYS 78 W CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 67 W CYS 57 1_555 B SG CYS 112 W CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 71 W CYS 61 1_555 B SG CYS 114 W CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 C SG CYS 27 X CYS 53 1_555 C SG CYS 81 X CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf10 C SG CYS 132 X CYS 158 1_555 C SG CYS 181 X CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 C SG CYS 226 X CYS 252 1_555 C SG CYS 285 X CYS 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 C SG CYS 428 X CYS 454 1_555 C SG CYS 509 X CYS 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf13 C SG CYS 551 X CYS 577 1_555 C SG CYS 610 X CYS 636 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf14 D SG CYS 27 Y CYS 53 1_555 D SG CYS 81 Y CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 D SG CYS 132 Y CYS 158 1_555 D SG CYS 181 Y CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 D SG CYS 226 Y CYS 252 1_555 D SG CYS 285 Y CYS 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 D SG CYS 428 Y CYS 454 1_555 D SG CYS 509 Y CYS 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf18 D SG CYS 551 Y CYS 577 1_555 D SG CYS 610 Y CYS 636 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 85 V ASN 75 1_555 G C1 NAG . V NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 B ND2 ASN 85 W ASN 75 1_555 H C1 NAG . W NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 C ND2 ASN 74 X ASN 100 1_555 E C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 C CE1 HIS 75 X HIS 101 1_555 E O7 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale5 C ND2 ASN 170 X ASN 196 1_555 I C1 NAG . X NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 C ND2 ASN 225 X ASN 251 1_555 J C1 NAG . X NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 C ND2 ASN 297 X ASN 323 1_555 K C1 NAG . X NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 C ND2 ASN 376 X ASN 402 1_555 L C1 NAG . X NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale9 C ND2 ASN 391 X ASN 417 1_555 M C1 NAG . X NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 C ND2 ASN 521 X ASN 547 1_555 N C1 NAG . X NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 C ND2 ASN 599 X ASN 625 1_555 O C1 NAG . X NAG 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale12 D ND2 ASN 74 Y ASN 100 1_555 Q C1 NAG . Y NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 D ND2 ASN 138 Y ASN 164 1_555 R C1 NAG . Y NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale14 D ND2 ASN 170 Y ASN 196 1_555 F C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale15 D ND2 ASN 225 Y ASN 251 1_555 S C1 NAG . Y NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale16 D ND2 ASN 297 Y ASN 323 1_555 T C1 NAG . Y NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale17 D ND2 ASN 376 Y ASN 402 1_555 U C1 NAG . Y NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale18 D ND2 ASN 391 Y ASN 417 1_555 V C1 NAG . Y NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 D ND2 ASN 521 Y ASN 547 1_555 W C1 NAG . Y NAG 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale20 D ND2 ASN 599 Y ASN 625 1_555 X C1 NAG . Y NAG 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale21 E O4 NAG . A NAG 1 1_555 E C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale22 F O4 NAG . B NAG 1 1_555 F C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 5T89 _atom_sites.fract_transf_matrix[1][1] 0.005998 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002132 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008124 _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] 0.006341 _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 V 1 201 109 NAG NAG . H 4 NAG W 1 201 109 NAG NAG . I 4 NAG X 1 703 702 NAG NAG . J 4 NAG X 1 704 703 NAG NAG . K 4 NAG X 1 705 704 NAG NAG . L 4 NAG X 1 706 705 NAG NAG . M 4 NAG X 1 707 706 NAG NAG . N 4 NAG X 1 708 708 NAG NAG . O 4 NAG X 1 709 711 NAG NAG . P 4 NAG X 1 710 801 NAG NAG . Q 4 NAG Y 1 701 700 NAG NAG . R 4 NAG Y 1 702 701 NAG NAG . S 4 NAG Y 1 705 703 NAG NAG . T 4 NAG Y 1 706 704 NAG NAG . U 4 NAG Y 1 707 705 NAG NAG . V 4 NAG Y 1 708 706 NAG NAG . W 4 NAG Y 1 709 708 NAG NAG . X 4 NAG Y 1 710 711 NAG NAG . Y 4 NAG Y 1 711 801 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 . . . S 4 -43.746 22.036 32.765 1 255.34 ? C1 NAG 705 Y 1 HETATM 2 C C2 NAG . . . S 4 -42.301 22.241 33.215 1 255.34 ? C2 NAG 705 Y 1 HETATM 3 C C3 NAG . . . S 4 -42.239 22.388 34.733 1 255.34 ? C3 NAG 705 Y 1 HETATM 4 C C4 NAG . . . S 4 -43.182 23.489 35.199 1 255.34 ? C4 NAG 705 Y 1 HETATM 5 C C5 NAG . . . S 4 -44.59 23.244 34.665 1 255.34 ? C5 NAG 705 Y 1 HETATM 6 C C6 NAG . . . S 4 -45.539 24.378 34.974 1 255.34 ? C6 NAG 705 Y 1 HETATM 7 C C7 NAG . . . S 4 -40.454 21.302 31.894 1 255.34 ? C7 NAG 705 Y 1 HETATM 8 C C8 NAG . . . S 4 -39.682 20.063 31.551 1 255.34 ? C8 NAG 705 Y 1 HETATM 9 N N2 NAG . . . S 4 -41.453 21.146 32.771 1 255.34 ? N2 NAG 705 Y 1 HETATM 10 O O3 NAG . . . S 4 -40.906 22.693 35.128 1 255.34 ? O3 NAG 705 Y 1 HETATM 11 O O4 NAG . . . S 4 -43.223 23.531 36.621 1 255.34 ? O4 NAG 705 Y 1 HETATM 12 O O5 NAG . . . S 4 -44.555 23.116 33.235 1 255.34 ? O5 NAG 705 Y 1 HETATM 13 O O6 NAG . . . S 4 -44.916 25.641 34.777 1 255.34 ? O6 NAG 705 Y 1 HETATM 14 O O7 NAG . . . S 4 -40.187 22.393 31.401 1 255.34 ? O7 NAG 705 Y 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #