data_8SM2 # _model_server_result.job_id ezGFsO53BNd_tSPNrrn4jQ _model_server_result.datetime_utc '2024-10-10 07:28:32' _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 8sm2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":703}' # _entry.id 8SM2 # _exptl.entry_id 8SM2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 90 _cell.angle_gamma 90 _cell.entry_id 8SM2 _cell.length_a 160.047 _cell.length_b 160.047 _cell.length_c 52.563 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SM2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -26.2815 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN MAN C1 O1 . O3 HO3 . sing 4 ? 3 5 3 BMA MAN C1 O1 . O6 HO6 . 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 C NAG 1 G 1 NAG G 1 NAG 3 n C NAG 2 G 2 NAG G 2 NAG 3 n C MAN 3 G 3 MAN G 3 MAN 3 n C MAN 4 G 4 MAN G 4 MAN 3 n C BMA 5 G 5 BMA G 5 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 28 A CYS 266 1_555 A SG CYS 85 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 61 A CYS 299 1_555 A SG CYS 63 A CYS 301 8_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 131 A CYS 369 1_555 A SG CYS 194 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 B SG CYS 28 C CYS 28 1_555 B SG CYS 79 C CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 B SG CYS 125 C CYS 125 1_555 B SG CYS 172 C CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 25 A ASN 263 1_555 C C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale2 B ND2 ASN 44 C ASN 44 1_555 D C1 NAG . C NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B ND2 ASN 58 C ASN 58 1_555 E C1 NAG . C NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale4 B ND2 ASN 120 C ASN 120 1_555 F C1 NAG . C NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 B ND2 ASN 156 C ASN 156 1_555 G C1 NAG . C NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 C O4 NAG . G NAG 1 1_555 C C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale7 C O4 NAG . G NAG 2 1_555 C C1 MAN . G MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 C O3 MAN . G MAN 3 1_555 C C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale9 C O6 MAN . G MAN 3 1_555 C C1 BMA . G BMA 5 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 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 8SM2 _atom_sites.fract_transf_matrix[1][1] 0.006248 _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] 0.006248 _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] 0.019025 _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 D 4 NAG C 1 701 701 NAG NAG . E 4 NAG C 1 702 702 NAG NAG . F 4 NAG C 1 703 703 NAG NAG . G 4 NAG C 1 704 704 NAG NAG . H 5 SO4 C 1 705 1 SO4 SO4 . # 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 4 -47.673 -28.452 31.832 1 271.66 ? C1 NAG 703 C 1 HETATM 2 C C2 NAG . . . F 4 -47.544 -29.787 32.573 1 275.79 ? C2 NAG 703 C 1 HETATM 3 C C3 NAG . . . F 4 -48.433 -30.838 31.921 1 285.08 ? C3 NAG 703 C 1 HETATM 4 C C4 NAG . . . F 4 -49.871 -30.345 31.854 1 281.1 ? C4 NAG 703 C 1 HETATM 5 C C5 NAG . . . F 4 -49.928 -28.997 31.14 1 275.87 ? C5 NAG 703 C 1 HETATM 6 C C6 NAG . . . F 4 -51.308 -28.383 31.155 1 267 ? C6 NAG 703 C 1 HETATM 7 C C7 NAG . . . F 4 -45.499 -30.452 33.754 1 255.04 ? C7 NAG 703 C 1 HETATM 8 C C8 NAG . . . F 4 -46.252 -30.164 35.019 1 243.21 ? C8 NAG 703 C 1 HETATM 9 N N2 NAG . . . F 4 -46.165 -30.245 32.614 1 271.69 ? N2 NAG 703 C 1 HETATM 10 O O3 NAG . . . F 4 -48.36 -32.051 32.66 1 298.5 ? O3 NAG 703 C 1 HETATM 11 O O4 NAG . . . F 4 -50.669 -31.288 31.148 1 285.25 ? O4 NAG 703 C 1 HETATM 12 O O5 NAG . . . F 4 -49.055 -28.057 31.787 1 274.08 ? O5 NAG 703 C 1 HETATM 13 O O6 NAG . . . F 4 -51.987 -28.682 32.367 1 270.71 ? O6 NAG 703 C 1 HETATM 14 O O7 NAG . . . F 4 -44.336 -30.842 33.764 1 250.25 ? O7 NAG 703 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #