data_3MBE # _model_server_result.job_id mf59ZRSR_mIoEpU25wFYsA _model_server_result.datetime_utc '2024-11-17 14:18:17' _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 3mbe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":300}' # _entry.id 3MBE # _exptl.entry_id 3MBE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _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 3MBE _cell.length_a 67.468 _cell.length_b 99.391 _cell.length_c 404.677 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MBE _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? pentameric 5 author_defined_assembly 1 ? pentameric 5 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,D,E,K,M 1 1 F,G,H,I,J,L,N 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 M N N ? 7 N N N # _pdbx_entity_branch.entity_id 6 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 6 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 6 n K NAG 1 I 1 NAG D 300 NAG 6 n K NAG 2 I 2 NAG D 301 NAG 6 n L NAG 1 J 1 NAG H 300 NAG 6 n L NAG 2 J 2 NAG H 301 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 111 A CYS 107 1_555 A SG CYS 167 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 B SG CYS 21 B CYS 15 1_555 B SG CYS 83 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 B SG CYS 122 B CYS 117 1_555 B SG CYS 178 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf4 D SG CYS 23 C CYS 23 1_555 D SG CYS 87 C CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 D SG CYS 133 C CYS 151 1_555 D SG CYS 183 C CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 D SG CYS 158 C CYS 176 1_555 E SG CYS 170 D CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf7 E SG CYS 23 D CYS 23 1_555 E SG CYS 91 D CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf8 E SG CYS 144 D CYS 158 1_555 E SG CYS 205 D CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf9 F SG CYS 111 E CYS 107 1_555 F SG CYS 167 E CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf10 G SG CYS 21 F CYS 15 1_555 G SG CYS 83 F CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 G SG CYS 122 F CYS 117 1_555 G SG CYS 178 F CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf12 I SG CYS 23 G CYS 23 1_555 I SG CYS 87 G CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 I SG CYS 133 G CYS 151 1_555 I SG CYS 183 G CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf14 I SG CYS 158 G CYS 176 1_555 J SG CYS 170 H CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf15 J SG CYS 23 H CYS 23 1_555 J SG CYS 91 H CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf16 J SG CYS 144 H CYS 158 1_555 J SG CYS 205 H CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? covale ? covale1 A ND2 ASN 122 A ASN 118 1_555 M C1 NAG . A NAG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 E ND2 ASN 229 D ASN 243 1_555 K C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale3 F ND2 ASN 122 E ASN 118 1_555 N C1 NAG . E NAG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 J ND2 ASN 229 H ASN 243 1_555 L C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale5 K O4 NAG . I NAG 1 1_555 K C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale6 L O4 NAG . J NAG 1 1_555 L C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 3MBE _atom_sites.fract_transf_matrix[1][1] 0.014822 _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] 0.010061 _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] 0.002471 _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 M 7 NAG A 1 300 300 NAG NAG . N 7 NAG E 1 300 300 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 . . . M 7 -49.722 -5.523 -91.659 1 120.85 ? C1 NAG 300 A 1 HETATM 2 C C2 NAG . . . M 7 -50.735 -4.916 -92.636 1 121.84 ? C2 NAG 300 A 1 HETATM 3 C C3 NAG . . . M 7 -52.152 -4.742 -92.078 1 121.91 ? C3 NAG 300 A 1 HETATM 4 C C4 NAG . . . M 7 -52.572 -5.86 -91.124 1 121.15 ? C4 NAG 300 A 1 HETATM 5 C C5 NAG . . . M 7 -51.45 -6.167 -90.151 1 120.23 ? C5 NAG 300 A 1 HETATM 6 C C6 NAG . . . M 7 -51.878 -7.249 -89.166 1 119.54 ? C6 NAG 300 A 1 HETATM 7 C C7 NAG . . . M 7 -50.712 -2.458 -92.839 1 122.69 ? C7 NAG 300 A 1 HETATM 8 C C8 NAG . . . M 7 -51.568 -1.771 -93.87 1 123.79 ? C8 NAG 300 A 1 HETATM 9 N N2 NAG . . . M 7 -50.216 -3.655 -93.151 1 122.4 ? N2 NAG 300 A 1 HETATM 10 O O3 NAG . . . M 7 -53.052 -4.713 -93.173 1 122.82 ? O3 NAG 300 A 1 HETATM 11 O O4 NAG . . . M 7 -53.729 -5.497 -90.398 1 121.12 ? O4 NAG 300 A 1 HETATM 12 O O5 NAG . . . M 7 -50.28 -6.551 -90.851 1 120.25 ? O5 NAG 300 A 1 HETATM 13 O O6 NAG . . . M 7 -52.708 -8.189 -89.819 1 119.9 ? O6 NAG 300 A 1 HETATM 14 O O7 NAG . . . M 7 -50.492 -1.914 -91.758 1 122.13 ? O7 NAG 300 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #