data_6Y5F # _model_server_result.job_id jKB_1Q5x34kJzM4pkRiQqQ _model_server_result.datetime_utc '2025-07-15 02:16:24' _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 6y5f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1201}' # _entry.id 6Y5F # _exptl.entry_id 6Y5F _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 6Y5F _cell.length_a 188.505 _cell.length_b 188.505 _cell.length_c 117.278 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y5F _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id E _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 3 ? 2 4 3 MAN BMA C1 O1 . 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 2 n C NAG 1 C 1 NAG A 404 NAG 2 n C NAG 2 C 2 NAG A 405 NAG 2 n C BMA 3 C 3 BMA A 406 BMA 2 n C MAN 4 C 4 MAN A 407 MAN 2 n D NAG 1 D 1 NAG A 408 NAG 2 n D NAG 2 D 2 NAG A 409 NAG 2 n D BMA 3 D 3 BMA A 410 BMA 2 n D MAN 4 D 4 MAN A 411 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 10 A CYS 30 1_555 A SG CYS 135 A CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 44 A CYS 64 1_555 A SG CYS 141 A CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 A SG CYS 93 A CYS 113 1_555 A SG CYS 112 A CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf4 A SG CYS 117 A CYS 137 1_555 A SG CYS 122 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 A SG CYS 159 A CYS 179 1_555 A SG CYS 169 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf6 A SG CYS 194 A CYS 214 1_555 A SG CYS 230 A CYS 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf7 A SG CYS 219 A CYS 239 1_555 A SG CYS 334 A CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 B SG CYS 485 B CYS 738 1_555 B SG CYS 520 B CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf9 B SG CYS 489 B CYS 742 1_555 B SG CYS 527 B CYS 780 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf10 B SG CYS 501 B CYS 754 1_555 B SG CYS 634 B CYS 887 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 B SG CYS 515 B CYS 768 1_555 B SG CYS 645 B CYS 898 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf12 B SG CYS 530 B CYS 783 1_555 B SG CYS 653 B CYS 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf13 B SG CYS 556 B CYS 809 1_555 B SG CYS 565 B CYS 818 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf14 B SG CYS 573 B CYS 826 1_555 B SG CYS 582 B CYS 835 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf15 B SG CYS 613 B CYS 866 1_555 B SG CYS 617 B CYS 870 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf16 B SG CYS 719 B CYS 972 1_555 B SG CYS 749 B CYS 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf17 B SG CYS 742 B CYS 995 1_555 B SG CYS 794 B CYS 1047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf18 B SG CYS 759 B CYS 1012 1_555 B SG CYS 764 B CYS 1017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf19 B SG CYS 795 B CYS 1048 1_555 B SG CYS 800 B CYS 1053 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf20 B SG CYS 834 B CYS 1087 1_555 B SG CYS 838 B CYS 1091 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 118 A ASN 138 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 330 A ASN 350 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale8 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _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 6Y5F _atom_sites.fract_transf_matrix[1][1] 0.005305 _atom_sites.fract_transf_matrix[1][2] 0.003063 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006126 _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] 0.008527 _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 E 3 NAG B 1 1201 1172 NAG NAG . F 4 PO4 B 1 1202 1 PO4 PO4 . G 4 PO4 B 1 1203 2 PO4 PO4 . H 5 HOH A 1 1101 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 . . . E 3 69.561 -78.095 18.794 1 102.25 ? C1 NAG 1201 B 1 HETATM 2 C C2 NAG . . . E 3 69.714 -79.161 19.879 1 129.2 ? C2 NAG 1201 B 1 HETATM 3 C C3 NAG . . . E 3 69.568 -78.54 21.273 1 131.14 ? C3 NAG 1201 B 1 HETATM 4 C C4 NAG . . . E 3 70.488 -77.337 21.428 1 138.69 ? C4 NAG 1201 B 1 HETATM 5 C C5 NAG . . . E 3 70.274 -76.365 20.271 1 133.39 ? C5 NAG 1201 B 1 HETATM 6 C C6 NAG . . . E 3 71.219 -75.189 20.298 1 127.27 ? C6 NAG 1201 B 1 HETATM 7 C C7 NAG . . . E 3 69.001 -81.329 18.978 1 123.94 ? C7 NAG 1201 B 1 HETATM 8 C C8 NAG . . . E 3 67.886 -82.328 18.887 1 85.19 ? C8 NAG 1201 B 1 HETATM 9 N N2 NAG . . . E 3 68.743 -80.226 19.689 1 138.36 ? N2 NAG 1201 B 1 HETATM 10 O O3 NAG . . . E 3 69.892 -79.5 22.273 1 124.33 ? O3 NAG 1201 B 1 HETATM 11 O O4 NAG . . . E 3 70.24 -76.696 22.677 1 119.68 ? O4 NAG 1201 B 1 HETATM 12 O O5 NAG . . . E 3 70.487 -77.043 19.023 1 122.05 ? O5 NAG 1201 B 1 HETATM 13 O O6 NAG . . . E 3 70.566 -73.994 19.891 1 132.49 ? O6 NAG 1201 B 1 HETATM 14 O O7 NAG . . . E 3 70.087 -81.514 18.439 1 126.85 ? O7 NAG 1201 B 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 848 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #