data_5D6D # _model_server_result.job_id BSfTufD6EWM6EB4_CDECvw _model_server_result.datetime_utc '2024-12-25 05:50:06' _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 5d6d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 5D6D # _exptl.entry_id 5D6D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 5D6D _cell.length_a 74.38 _cell.length_b 94.5 _cell.length_c 108.67 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D6D _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 ? 6 G N N ? 6 H 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 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 3 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 3 6 5 GAL NAG C1 O1 . O4 HO4 . sing 6 ? 3 7 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 3 8 7 NAG MAN C1 O1 . O2 HO2 . sing 8 ? 3 9 1 FUL NAG C1 O1 . O6 HO6 . sing 9 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 10 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 11 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 12 ? 4 5 4 NAG MAN C1 O1 . O2 HO2 . sing 13 ? 4 6 5 GAL NAG C1 O1 . O4 HO4 . sing 14 ? 4 7 3 MAN BMA C1 O1 . O3 HO3 . sing 15 ? 4 8 7 NAG MAN C1 O1 . O2 HO2 . 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 D NAG 1 D 1 NAG B 1 NAG 3 n D NAG 2 D 2 NAG B 2 NAG 3 n D BMA 3 D 3 BMA B 3 BMA 3 n D MAN 4 D 4 MAN B 4 MAN 3 n D NAG 5 D 5 NAG B 5 NAG 3 n D GAL 6 D 6 GAL B 7 GAL 3 n D MAN 7 D 7 MAN B 6 MAN 3 n D NAG 8 D 8 NAG B 9 NAG 3 n D FUL 9 D 9 FUL B 8 FUL 4 n E NAG 1 E 1 NAG A 1 NAG 4 n E NAG 2 E 2 NAG A 2 NAG 4 n E BMA 3 E 3 BMA A 3 BMA 4 n E MAN 4 E 4 MAN A 4 MAN 4 n E NAG 5 E 5 NAG A 5 NAG 4 n E GAL 6 E 6 GAL A 7 GAL 4 n E MAN 7 E 7 MAN A 6 MAN 4 n E NAG 8 E 8 NAG A 9 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 64 A CYS 261 1_555 A SG CYS 124 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? disulf ? disulf2 A SG CYS 170 A CYS 367 1_555 A SG CYS 228 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf3 B SG CYS 64 B CYS 261 1_555 B SG CYS 124 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 170 B CYS 367 1_555 B SG CYS 228 B CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? disulf ? disulf5 C SG CYS 47 C CYS 29 1_555 C SG CYS 89 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? disulf ? disulf6 C SG CYS 128 C CYS 110 1_555 C SG CYS 172 C CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 100 A ASN 297 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.257 ? covale ? covale2 B ND2 ASN 100 B ASN 297 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? covale ? covale3 C ND2 ASN 63 C ASN 45 1_555 H C1 NAG . C NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale4 C ND2 ASN 180 C ASN 162 1_555 G C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.559 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale6 D O6 NAG . D NAG 1 1_555 D C1 FUL . D FUL 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.29 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale8 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale9 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale10 D O2 MAN . D MAN 4 1_555 D C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale11 D O4 NAG . D NAG 5 1_555 D C1 GAL . D GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale12 D O2 MAN . D MAN 7 1_555 D C1 NAG . D NAG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.26 ? covale ? covale13 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale14 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale15 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale16 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale17 E O2 MAN . E MAN 4 1_555 E C1 NAG . E NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale18 E O4 NAG . E NAG 5 1_555 E C1 GAL . E GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale19 E O2 MAN . E MAN 7 1_555 E C1 NAG . E NAG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? # _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 353 n n C1 O1 NAG sing 354 n n C1 O5 NAG sing 355 n n C1 H1 NAG sing 356 n n C2 C3 NAG sing 357 n n C2 N2 NAG sing 358 n n C2 H2 NAG sing 359 n n C3 C4 NAG sing 360 n n C3 O3 NAG sing 361 n n C3 H3 NAG sing 362 n n C4 C5 NAG sing 363 n n C4 O4 NAG sing 364 n n C4 H4 NAG sing 365 n n C5 C6 NAG sing 366 n n C5 O5 NAG sing 367 n n C5 H5 NAG sing 368 n n C6 O6 NAG sing 369 n n C6 H61 NAG sing 370 n n C6 H62 NAG sing 371 n n C7 C8 NAG sing 372 n n C7 N2 NAG sing 373 n n C7 O7 NAG doub 374 n n C8 H81 NAG sing 375 n n C8 H82 NAG sing 376 n n C8 H83 NAG sing 377 n n N2 HN2 NAG sing 378 n n O1 HO1 NAG sing 379 n n O3 HO3 NAG sing 380 n n O4 HO4 NAG sing 381 n n O6 HO6 NAG sing 382 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 5D6D _atom_sites.fract_transf_matrix[1][1] 0.013445 _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] 0.010582 _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] 0.009202 _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 FUC B 1 509 508 FUC FUC . G 6 NAG C 1 301 301 NAG NAG . H 6 NAG C 1 302 1460 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 . . . G 6 -3.084 24.357 -33.377 1 39.4 ? C1 NAG 301 C 1 HETATM 2 C C2 NAG . . . G 6 -2.56 25.491 -32.507 1 41.46 ? C2 NAG 301 C 1 HETATM 3 C C3 NAG . . . G 6 -1.252 24.93 -31.968 1 47.74 ? C3 NAG 301 C 1 HETATM 4 C C4 NAG . . . G 6 -1.51 23.557 -31.327 1 53.96 ? C4 NAG 301 C 1 HETATM 5 C C5 NAG . . . G 6 -2.569 22.689 -32.05 1 42.26 ? C5 NAG 301 C 1 HETATM 6 C C6 NAG . . . G 6 -3.089 21.639 -31.075 1 46.27 ? C6 NAG 301 C 1 HETATM 7 C C7 NAG . . . G 6 -2.044 26.836 -34.591 1 35.49 ? C7 NAG 301 C 1 HETATM 8 C C8 NAG . . . G 6 -2.11 28.225 -35.181 1 30.82 ? C8 NAG 301 C 1 HETATM 9 N N2 NAG . . . G 6 -2.486 26.716 -33.31 1 38.65 ? N2 NAG 301 C 1 HETATM 10 O O3 NAG . . . G 6 -0.677 25.801 -31.032 1 45.89 ? O3 NAG 301 C 1 HETATM 11 O O4 NAG . . . G 6 -0.294 22.834 -31.297 1 68.13 ? O4 NAG 301 C 1 HETATM 12 O O5 NAG . . . G 6 -3.649 23.444 -32.605 1 40.27 ? O5 NAG 301 C 1 HETATM 13 O O6 NAG . . . G 6 -2.103 20.648 -30.964 1 67.43 ? O6 NAG 301 C 1 HETATM 14 O O7 NAG . . . G 6 -1.59 25.912 -35.29 1 37.21 ? O7 NAG 301 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #