data_5TGV # _model_server_result.job_id V610iuWn-Lklwr9OkD0zYA _model_server_result.datetime_utc '2025-01-11 14:52:34' _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 5tgv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":401}' # _entry.id 5TGV # _exptl.entry_id 5TGV _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111.97 _cell.angle_gamma 90 _cell.entry_id 5TGV _cell.length_a 63.512 _cell.length_b 253.173 _cell.length_c 69.964 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TGV _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 J N N ? 6 K N N ? 6 L N N ? 6 N N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 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 ? 4 2 1 GAL NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 SIA GAL C2 O2 . O3 HO3 . sing 4 ? 5 2 1 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 3 n G NAG 1 G 1 NAG G 401 NAG 3 n G NAG 2 G 2 NAG G 402 NAG 4 n H NAG 1 H 1 NAG L 502 NAG 4 n H GAL 2 H 2 GAL L 501 GAL 4 n H SIA 3 H 3 SIA L 500 SIA 5 n I NAG 1 I 1 NAG G 502 NAG 5 n I BMA 2 I 2 BMA G 503 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 8 A CYS 14 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 274 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 134 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf5 A SG CYS 278 A CYS 281 1_555 A SG CYS 302 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf6 B SG CYS 143 B CYS 144 1_555 B SG CYS 147 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf7 C SG CYS 8 C CYS 14 1_555 D SG CYS 136 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf8 C SG CYS 46 C CYS 52 1_555 C SG CYS 274 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf9 C SG CYS 58 C CYS 64 1_555 C SG CYS 70 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf10 C SG CYS 91 C CYS 97 1_555 C SG CYS 134 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf11 C SG CYS 278 C CYS 281 1_555 C SG CYS 302 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf12 D SG CYS 143 D CYS 144 1_555 D SG CYS 147 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf13 E SG CYS 8 E CYS 14 1_555 F SG CYS 136 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf14 E SG CYS 46 E CYS 52 1_555 E SG CYS 274 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf15 E SG CYS 58 E CYS 64 1_555 E SG CYS 70 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf16 E SG CYS 91 E CYS 97 1_555 E SG CYS 134 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf17 E SG CYS 278 E CYS 281 1_555 E SG CYS 302 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf18 F SG CYS 143 F CYS 144 1_555 F SG CYS 147 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? covale ? covale1 A ND2 ASN 32 A ASN 38 1_555 J C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 239 A ASN 242 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 C ND2 ASN 32 C ASN 38 1_555 K C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale4 C ND2 ASN 239 C ASN 242 1_555 L C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale5 E ND2 ASN 239 E ASN 242 1_555 N C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.241 ? covale ? covale7 H O4 NAG . H NAG 1 1_555 H C1 GAL . H GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.164 ? covale ? covale8 H O3 GAL . H GAL 2 1_555 H C2 SIA . H SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale9 I O4 NAG . I NAG 1 1_555 I C1 BMA . I BMA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 5TGV _atom_sites.fract_transf_matrix[1][1] 0.015745 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006352 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00395 _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] 0.015412 _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 J 6 NAG A 1 401 400 NAG NAG . K 6 NAG C 1 401 500 NAG NAG . L 6 NAG C 1 402 501 NAG NAG . M 7 SIA C 1 405 600 SIA SIA . N 6 NAG E 1 601 601 NAG NAG . O 7 SIA E 1 602 700 SIA SIA . # 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 . . . K 6 91.595 -4.924 128.629 1 89.01 ? C1 NAG 401 C 1 HETATM 2 C C2 NAG . . . K 6 91.119 -5.718 127.43 1 89.54 ? C2 NAG 401 C 1 HETATM 3 C C3 NAG . . . K 6 91.593 -5.053 126.143 1 93.8 ? C3 NAG 401 C 1 HETATM 4 C C4 NAG . . . K 6 91.253 -3.564 126.132 1 97.41 ? C4 NAG 401 C 1 HETATM 5 C C5 NAG . . . K 6 91.579 -2.875 127.459 1 94.1 ? C5 NAG 401 C 1 HETATM 6 C C6 NAG . . . K 6 90.904 -1.513 127.596 1 99.44 ? C6 NAG 401 C 1 HETATM 7 C C7 NAG . . . K 6 91.88 -7.884 128.201 1 90.28 ? C7 NAG 401 C 1 HETATM 8 C C8 NAG . . . K 6 90.507 -8.438 128.368 1 69.17 ? C8 NAG 401 C 1 HETATM 9 N N2 NAG . . . K 6 91.957 -6.889 127.366 1 91.68 ? N2 NAG 401 C 1 HETATM 10 O O3 NAG . . . K 6 91.035 -5.663 124.988 1 90.03 ? O3 NAG 401 C 1 HETATM 11 O O4 NAG . . . K 6 91.877 -2.898 125.031 1 96.01 ? O4 NAG 401 C 1 HETATM 12 O O5 NAG . . . K 6 91.074 -3.633 128.567 1 89.06 ? O5 NAG 401 C 1 HETATM 13 O O6 NAG . . . K 6 89.768 -1.619 128.471 1 95.91 ? O6 NAG 401 C 1 HETATM 14 O O7 NAG . . . K 6 92.859 -8.29 128.772 1 85.84 ? O7 NAG 401 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #