data_6IOM # _model_server_result.job_id '_rLUGyHZMxEjFUWi6VBnLg' _model_server_result.datetime_utc '2024-11-26 05:30:37' _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 6iom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1002}' # _entry.id 6IOM # _exptl.entry_id 6IOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 6IOM _cell.length_a 57.055 _cell.length_b 120.156 _cell.length_c 169.431 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IOM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,E,F,G 1 1 B,D,H,I 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 ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n C NAG 1 C 1 NAG A 1003 NAG 2 n C NAG 2 C 2 NAG A 1004 NAG 2 n D NAG 1 D 1 NAG B 1002 NAG 2 n D NAG 2 D 2 NAG B 1003 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 3 A CYS 3 1_555 A SG CYS 31 A CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 6 A CYS 6 1_555 A SG CYS 14 A CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? disulf ? disulf3 A SG CYS 24 A CYS 24 1_555 A SG CYS 52 A CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? disulf ? disulf4 A SG CYS 78 A CYS 78 1_555 A SG CYS 83 A CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf5 A SG CYS 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 A SG CYS 113 A CYS 113 1_555 A SG CYS 121 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 A SG CYS 131 A CYS 131 1_555 A SG CYS 163 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf8 A SG CYS 169 A CYS 169 1_555 A SG CYS 185 A CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf9 A SG CYS 186 A CYS 186 1_555 A SG CYS 191 A CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf10 B SG CYS 3 B CYS 3 1_555 B SG CYS 31 B CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? disulf ? disulf11 B SG CYS 24 B CYS 24 1_555 B SG CYS 52 B CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf12 B SG CYS 78 B CYS 78 1_555 B SG CYS 83 B CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf13 B SG CYS 110 B CYS 110 1_555 B SG CYS 142 B CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf14 B SG CYS 113 B CYS 113 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf15 B SG CYS 131 B CYS 131 1_555 B SG CYS 163 B CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? disulf ? disulf16 B SG CYS 169 B CYS 169 1_555 B SG CYS 185 B CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? disulf ? disulf17 B SG CYS 186 B CYS 186 1_555 B SG CYS 191 B CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? covale ? covale1 A ND2 ASN 88 A ASN 88 1_555 E C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale2 A ND2 ASN 133 A ASN 133 1_555 F C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 A ND2 ASN 146 A ASN 146 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale4 A ND2 ASN 153 A ASN 153 1_555 G C1 NAG . A NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 B ND2 ASN 133 B ASN 133 1_555 I C1 NAG . B NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 B ND2 ASN 146 B ASN 146 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale7 B ND2 ASN 153 B ASN 153 1_555 H C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? # _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 6IOM _atom_sites.fract_transf_matrix[1][1] 0.017527 _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] 0.008323 _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] 0.005902 _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 E 3 NAG A 1 1001 1001 NAG NAG . F 3 NAG A 1 1002 1002 NAG NAG . G 3 NAG A 1 1005 1005 NAG NAG . H 3 NAG B 1 301 1004 NAG NAG . I 3 NAG B 1 304 1001 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 . . . F 3 32.59 79.655 58.303 1 95.46 ? C1 NAG 1002 A 1 HETATM 2 C C2 NAG . . . F 3 32.818 81.074 58.784 1 106.71 ? C2 NAG 1002 A 1 HETATM 3 C C3 NAG . . . F 3 32.16 82.033 57.8 1 118.75 ? C3 NAG 1002 A 1 HETATM 4 C C4 NAG . . . F 3 32.649 81.739 56.38 1 125.82 ? C4 NAG 1002 A 1 HETATM 5 C C5 NAG . . . F 3 32.622 80.235 56.049 1 118.74 ? C5 NAG 1002 A 1 HETATM 6 C C6 NAG . . . F 3 33.279 79.897 54.728 1 119.32 ? C6 NAG 1002 A 1 HETATM 7 C C7 NAG . . . F 3 33.028 81.701 61.169 1 107.45 ? C7 NAG 1002 A 1 HETATM 8 C C8 NAG . . . F 3 32.293 81.847 62.467 1 107 ? C8 NAG 1002 A 1 HETATM 9 N N2 NAG . . . F 3 32.296 81.269 60.13 1 108.8 ? N2 NAG 1002 A 1 HETATM 10 O O3 NAG . . . F 3 32.417 83.389 58.155 1 120.05 ? O3 NAG 1002 A 1 HETATM 11 O O4 NAG . . . F 3 31.853 82.442 55.43 1 131.12 ? O4 NAG 1002 A 1 HETATM 12 O O5 NAG . . . F 3 33.269 79.457 57.074 1 111.32 ? O5 NAG 1002 A 1 HETATM 13 O O6 NAG . . . F 3 32.364 79.245 53.857 1 123.51 ? O6 NAG 1002 A 1 HETATM 14 O O7 NAG . . . F 3 34.23 81.957 61.069 1 105.49 ? O7 NAG 1002 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #