data_7VN9 # _model_server_result.job_id Pwt0szj0JJ-EOx5Q4lx88g _model_server_result.datetime_utc '2024-10-15 13:21:33' _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 7vn9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 7VN9 # _exptl.entry_id 7VN9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _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 7VN9 _cell.length_a 183.732 _cell.length_b 183.732 _cell.length_c 255.988 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VN9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 62 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_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,G,H 1 1 D,E,F,I,J 2 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 6 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 2 1 NAG 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 4 n G NAG 1 D 1 NAG E 436 NAG 4 n G NAG 2 D 2 NAG E 437 NAG 4 n G BMA 3 D 3 BMA E 438 BMA 5 n H NAG 1 F 1 NAG E 439 NAG 5 n H NAG 2 F 2 NAG E 440 NAG 4 n I NAG 1 G 1 NAG C 432 NAG 4 n I NAG 2 G 2 NAG C 433 NAG 4 n I BMA 3 G 3 BMA C 434 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 22 H CYS 22 1_555 A SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf2 A SG CYS 150 H CYS 150 1_555 A SG CYS 206 H CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 134 L CYS 134 1_555 B SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 C SG CYS 24 E CYS 317 1_555 C SG CYS 27 E CYS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 C SG CYS 47 E CYS 340 1_555 C SG CYS 93 E CYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf7 C SG CYS 76 E CYS 369 1_555 C SG CYS 103 E CYS 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? disulf ? disulf8 D SG CYS 22 A CYS 22 1_555 D SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 D SG CYS 150 A CYS 150 1_555 D SG CYS 206 A CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf10 E SG CYS 23 B CYS 23 1_555 E SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf11 E SG CYS 134 B CYS 134 1_555 E SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf12 F SG CYS 24 C CYS 317 1_555 F SG CYS 27 C CYS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf13 F SG CYS 47 C CYS 340 1_555 F SG CYS 93 C CYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf14 F SG CYS 76 C CYS 369 1_555 F SG CYS 103 C CYS 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? covale ? covale1 C ND2 ASN 33 E ASN 326 1_555 G C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale2 C ND2 ASN 40 E ASN 333 1_555 H C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale3 F ND2 ASN 33 C ASN 326 1_555 I C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale4 F ND2 ASN 40 C ASN 333 1_555 J C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale5 G O4 NAG . D NAG 1 1_555 G C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale6 G O4 NAG . D NAG 2 1_555 G C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 H O4 NAG . F NAG 1 1_555 H C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale8 I O4 NAG . G NAG 1 1_555 I C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 I O4 NAG . G NAG 2 1_555 I C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 7VN9 _atom_sites.fract_transf_matrix[1][1] 0.005443 _atom_sites.fract_transf_matrix[1][2] 0.003142 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006285 _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] 0.003906 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id J _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id C _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 501 _pdbx_nonpoly_scheme.auth_seq_num 435 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . J 6 29.901 30.036 66.302 1 230.38 ? C1 NAG 501 C 1 HETATM 2 C C2 NAG . . . J 6 30.974 28.954 66.128 1 231.28 ? C2 NAG 501 C 1 HETATM 3 C C3 NAG . . . J 6 30.458 27.883 65.15 1 232.37 ? C3 NAG 501 C 1 HETATM 4 C C4 NAG . . . J 6 29.126 27.314 65.641 1 232.85 ? C4 NAG 501 C 1 HETATM 5 C C5 NAG . . . J 6 28.102 28.422 65.937 1 231.9 ? C5 NAG 501 C 1 HETATM 6 C C6 NAG . . . J 6 26.841 27.884 66.599 1 232.35 ? C6 NAG 501 C 1 HETATM 7 C C7 NAG . . . J 6 33.377 29.542 66.379 1 230.75 ? C7 NAG 501 C 1 HETATM 8 C C8 NAG . . . J 6 34.539 30.231 65.728 1 230.27 ? C8 NAG 501 C 1 HETATM 9 N N2 NAG . . . J 6 32.232 29.537 65.673 1 230.83 ? N2 NAG 501 C 1 HETATM 10 O O3 NAG . . . J 6 31.384 26.81 65.011 1 233.32 ? O3 NAG 501 C 1 HETATM 11 O O4 NAG . . . J 6 28.574 26.427 64.67 1 233.84 ? O4 NAG 501 C 1 HETATM 12 O O5 NAG . . . J 6 28.653 29.418 66.822 1 230.88 ? O5 NAG 501 C 1 HETATM 13 O O6 NAG . . . J 6 27.02 27.509 67.963 1 232.45 ? O6 NAG 501 C 1 HETATM 14 O O7 NAG . . . J 6 33.475 29.008 67.487 1 231.1 ? O7 NAG 501 C 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #