data_7KBT # _model_server_result.job_id 8igUesc-sEH3war3TADGPA _model_server_result.datetime_utc '2024-12-26 23:19:29' _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 7kbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2401}' # _entry.id 7KBT # _exptl.entry_id 7KBT _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 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 90 _cell.entry_id 7KBT _cell.length_a 132.243 _cell.length_b 132.243 _cell.length_c 380.029 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KBT _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 G 1 NAG G 2328 NAG 4 n D NAG 2 G 2 NAG G 2329 NAG 4 n E NAG 1 B 1 NAG G 2343 NAG 4 n E NAG 2 B 2 NAG G 2344 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 173 A CYS 154 1_555 A SG CYS 199 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 268 A CYS 249 1_555 A SG CYS 349 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 A SG CYS 547 A CYS 528 1_555 A SG CYS 573 A CYS 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 A SG CYS 649 A CYS 630 1_555 A SG CYS 730 A CYS 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 967 A CYS 1832 1_555 A SG CYS 993 A CYS 1858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 1156 A CYS 2021 1_555 A SG CYS 1304 A CYS 2169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 B SG CYS 22 E CYS 22 1_555 B SG CYS 96 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 C SG CYS 23 F CYS 23 1_555 C SG CYS 88 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 259 A ASN 240 1_555 E C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 A ND2 ASN 945 A ASN 1810 1_555 F C1 NAG . A NAG 2401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 A ND2 ASN 1253 A ASN 2118 1_555 D C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 D O4 NAG . G NAG 1 1_555 D C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale5 E O4 NAG . B NAG 1 1_555 E C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? metalc ? metalc1 A O LYS 127 A LYS 108 1_555 I CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc2 A O GLU 142 A GLU 123 1_555 I CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc3 A OD2 ASP 145 A ASP 126 1_555 I CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.015 ? metalc ? metalc4 A OD1 ASP 146 A ASP 127 1_555 I CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc5 A ND1 HIS 287 A HIS 268 1_555 H ZN ZN . A ZN 2403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc6 A SG CYS 330 A CYS 311 1_555 H ZN ZN . A ZN 2403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc7 A ND1 HIS 337 A HIS 318 1_555 H ZN ZN . A ZN 2403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc8 A ND1 HIS 1089 A HIS 1954 1_555 G CU CU . A CU 2402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc9 A SG CYS 1135 A CYS 2000 1_555 G CU CU . A CU 2402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? # _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 7KBT _atom_sites.fract_transf_matrix[1][1] 0.007562 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007562 _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] 0.002631 _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 F 5 NAG A 1 2401 2345 NAG NAG . G 6 CU A 1 2402 1 CU CU . H 7 ZN A 1 2403 1 ZN ZN . I 8 CA A 1 2404 1 CA CA . # 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 . . . F 5 70.826 -29.863 19.091 1 290.23 ? C1 NAG 2401 A 1 HETATM 2 C C2 NAG . . . F 5 71.64 -29.699 20.376 1 296.35 ? C2 NAG 2401 A 1 HETATM 3 C C3 NAG . . . F 5 72.16 -31.059 20.851 1 300.55 ? C3 NAG 2401 A 1 HETATM 4 C C4 NAG . . . F 5 71.023 -32.068 20.955 1 298.99 ? C4 NAG 2401 A 1 HETATM 5 C C5 NAG . . . F 5 70.236 -32.126 19.648 1 290.13 ? C5 NAG 2401 A 1 HETATM 6 C C6 NAG . . . F 5 69.021 -33.022 19.722 1 291.77 ? C6 NAG 2401 A 1 HETATM 7 C C7 NAG . . . F 5 73.74 -28.91 19.325 1 288.47 ? C7 NAG 2401 A 1 HETATM 8 C C8 NAG . . . F 5 74.767 -27.819 19.312 1 273.19 ? C8 NAG 2401 A 1 HETATM 9 N N2 NAG . . . F 5 72.736 -28.756 20.201 1 293.63 ? N2 NAG 2401 A 1 HETATM 10 O O3 NAG . . . F 5 72.797 -30.913 22.115 1 302.97 ? O3 NAG 2401 A 1 HETATM 11 O O4 NAG . . . F 5 71.544 -33.361 21.242 1 300.51 ? O4 NAG 2401 A 1 HETATM 12 O O5 NAG . . . F 5 69.765 -30.814 19.308 1 282.73 ? O5 NAG 2401 A 1 HETATM 13 O O6 NAG . . . F 5 68.966 -33.733 20.951 1 300.26 ? O6 NAG 2401 A 1 HETATM 14 O O7 NAG . . . F 5 73.818 -29.883 18.578 1 291.89 ? O7 NAG 2401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 369 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 14 #