data_4GZ9 # _model_server_result.job_id tT2Uewa9Fu1kQXXIdQXTCA _model_server_result.datetime_utc '2025-02-18 20:05:55' _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 4gz9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":604}' # _entry.id 4GZ9 # _exptl.entry_id 4GZ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 4GZ9 _cell.length_a 245.359 _cell.length_b 245.359 _cell.length_c 47.93 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GZ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 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 1 1 A,B,C,D,E,F,G,H,I,J,K 2 1,2 # 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' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 47.93 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 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 2 n B NAG 1 B 1 NAG A 1150 NAG 2 n B NAG 2 B 2 NAG A 1151 NAG 2 n B BMA 3 B 3 BMA A 1152 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 9 A CYS 27 1_555 A SG CYS 36 A CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf2 A SG CYS 64 A CYS 82 1_555 A SG CYS 86 A CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf3 A SG CYS 129 A CYS 147 1_555 A SG CYS 155 A CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf4 A SG CYS 188 A CYS 206 1_555 A SG CYS 210 A CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf5 A SG CYS 257 A CYS 275 1_555 A SG CYS 406 A CYS 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? disulf ? disulf6 A SG CYS 413 A CYS 431 1_555 A SG CYS 565 A CYS 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? covale ? covale1 A ND2 ASN 132 A ASN 150 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 243 A ASN 261 1_555 C C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? metalc ? metalc1 A OE1 GLU 60 A GLU 78 1_555 E CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc2 A OD2 ASP 67 A ASP 85 1_555 E CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc3 A OD1 ASP 108 A ASP 126 1_555 E CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc4 A O GLU 110 A GLU 128 1_555 E CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc5 A O THR 111 A THR 129 1_555 E CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc6 A OE1 GLU 177 A GLU 195 1_555 D CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc7 A OD2 ASP 191 A ASP 209 1_555 D CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc8 A OD1 ASP 191 A ASP 209 1_555 D CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc9 A OD1 ASP 232 A ASP 250 1_555 D CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc10 A O ALA 234 A ALA 252 1_555 D CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc11 A O ILE 235 A ILE 253 1_555 D CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc12 D CA CA . A CA 605 1_555 K O HOH . A HOH 728 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc13 E CA CA . A CA 606 1_555 K O HOH . A HOH 729 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? # _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 270 n n C1 O1 NAG sing 271 n n C1 O5 NAG sing 272 n n C1 H1 NAG sing 273 n n C2 C3 NAG sing 274 n n C2 N2 NAG sing 275 n n C2 H2 NAG sing 276 n n C3 C4 NAG sing 277 n n C3 O3 NAG sing 278 n n C3 H3 NAG sing 279 n n C4 C5 NAG sing 280 n n C4 O4 NAG sing 281 n n C4 H4 NAG sing 282 n n C5 C6 NAG sing 283 n n C5 O5 NAG sing 284 n n C5 H5 NAG sing 285 n n C6 O6 NAG sing 286 n n C6 H61 NAG sing 287 n n C6 H62 NAG sing 288 n n C7 C8 NAG sing 289 n n C7 N2 NAG sing 290 n n C7 O7 NAG doub 291 n n C8 H81 NAG sing 292 n n C8 H82 NAG sing 293 n n C8 H83 NAG sing 294 n n N2 HN2 NAG sing 295 n n O1 HO1 NAG sing 296 n n O3 HO3 NAG sing 297 n n O4 HO4 NAG sing 298 n n O6 HO6 NAG sing 299 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 4GZ9 _atom_sites.fract_transf_matrix[1][1] 0.004076 _atom_sites.fract_transf_matrix[1][2] 0.002353 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004706 _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] 0.020864 _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 C 3 NAG A 1 604 1261 NAG NAG . D 4 CA A 1 605 1 CA CA . E 4 CA A 1 606 2 CA CA . F 5 SO4 A 1 607 1 SO4 SO4 . G 5 SO4 A 1 608 2 SO4 SO4 . H 6 EDO A 1 609 3318 EDO EDO . I 6 EDO A 1 610 3319 EDO EDO . J 6 EDO A 1 611 3320 EDO EDO . K 7 HOH A 1 701 1 HOH HOH . K 7 HOH A 2 702 2 HOH HOH . K 7 HOH A 3 703 3 HOH HOH . K 7 HOH A 4 704 4 HOH HOH . K 7 HOH A 5 705 5 HOH HOH . K 7 HOH A 6 706 6 HOH HOH . K 7 HOH A 7 707 7 HOH HOH . K 7 HOH A 8 708 8 HOH HOH . K 7 HOH A 9 709 9 HOH HOH . K 7 HOH A 10 710 10 HOH HOH . K 7 HOH A 11 711 11 HOH HOH . K 7 HOH A 12 712 12 HOH HOH . K 7 HOH A 13 713 13 HOH HOH . K 7 HOH A 14 714 14 HOH HOH . K 7 HOH A 15 715 15 HOH HOH . K 7 HOH A 16 716 16 HOH HOH . K 7 HOH A 17 717 17 HOH HOH . K 7 HOH A 18 718 18 HOH HOH . K 7 HOH A 19 719 20 HOH HOH . K 7 HOH A 20 720 21 HOH HOH . K 7 HOH A 21 721 22 HOH HOH . K 7 HOH A 22 722 23 HOH HOH . K 7 HOH A 23 723 24 HOH HOH . K 7 HOH A 24 724 26 HOH HOH . K 7 HOH A 25 725 29 HOH HOH . K 7 HOH A 26 726 30 HOH HOH . K 7 HOH A 27 727 32 HOH HOH . K 7 HOH A 28 728 1 HOH HOH . K 7 HOH A 29 729 2 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 . . . C 3 -75.672 47.56 9.37 1 91.54 ? C1 NAG 604 A 1 HETATM 2 C C2 NAG . . . C 3 -77.095 47.233 8.882 1 92.74 ? C2 NAG 604 A 1 HETATM 3 C C3 NAG . . . C 3 -77.646 45.954 9.497 1 98.28 ? C3 NAG 604 A 1 HETATM 4 C C4 NAG . . . C 3 -76.645 44.81 9.404 1 105.23 ? C4 NAG 604 A 1 HETATM 5 C C5 NAG . . . C 3 -75.271 45.232 9.919 1 103.88 ? C5 NAG 604 A 1 HETATM 6 C C6 NAG . . . C 3 -74.225 44.162 9.628 1 110.14 ? C6 NAG 604 A 1 HETATM 7 C C7 NAG . . . C 3 -78.391 49.236 8.226 1 83.53 ? C7 NAG 604 A 1 HETATM 8 C C8 NAG . . . C 3 -77.75 49.137 6.868 1 85.22 ? C8 NAG 604 A 1 HETATM 9 N N2 NAG . . . C 3 -78.047 48.316 9.136 1 87.83 ? N2 NAG 604 A 1 HETATM 10 O O3 NAG . . . C 3 -78.844 45.596 8.845 1 98.02 ? O3 NAG 604 A 1 HETATM 11 O O4 NAG . . . C 3 -77.13 43.754 10.203 1 113.07 ? O4 NAG 604 A 1 HETATM 12 O O5 NAG . . . C 3 -74.827 46.424 9.305 1 98.04 ? O5 NAG 604 A 1 HETATM 13 O O6 NAG . . . C 3 -73.098 44.753 9.018 1 110.52 ? O6 NAG 604 A 1 HETATM 14 O O7 NAG . . . C 3 -79.185 50.15 8.463 1 75.57 ? O7 NAG 604 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #