data_6OML # _model_server_result.job_id lVPrYBu0XR513c_lYs_4bw _model_server_result.datetime_utc '2024-11-28 08:39:10' _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 6oml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":901}' # _entry.id 6OML # _exptl.entry_id 6OML _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 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 90 _cell.entry_id 6OML _cell.length_a 67.779 _cell.length_b 67.779 _cell.length_c 148.011 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6OML _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 3 MAN BMA 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 2 n C NAG 1 A 1 NAG Y 901 NAG 2 n C NAG 2 A 2 NAG Y 902 NAG 2 n C BMA 3 A 3 BMA Y 903 BMA 2 n C MAN 4 A 4 MAN Y 907 MAN 2 n C MAN 5 A 5 MAN Y 908 MAN 2 n C MAN 6 A 6 MAN Y 904 MAN # 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 4 X CYS 14 1_555 A SG CYS 70 X CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 A SG CYS 33 X CYS 43 1_555 A SG CYS 102 X CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 37 X CYS 47 1_555 A SG CYS 104 X CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 A SG CYS 69 X CYS 78 1_555 B SG CYS 69 Y CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf5 B SG CYS 4 Y CYS 14 1_555 B SG CYS 70 Y CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 33 Y CYS 43 1_555 B SG CYS 102 Y CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf7 B SG CYS 37 Y CYS 47 1_555 B SG CYS 104 Y CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 46 X ASN 56 1_555 D C1 NAG . X NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale2 B ND2 ASN 46 Y ASN 56 1_555 C C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 C O4 NAG . A NAG 1 1_555 C C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale4 C O4 NAG . A NAG 2 1_555 C C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C O3 BMA . A BMA 3 1_555 C C1 MAN . A MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 C O6 BMA . A BMA 3 1_555 C C1 MAN . A MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale7 C O2 MAN . A MAN 4 1_555 C C1 MAN . A MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 6OML _atom_sites.fract_transf_matrix[1][1] 0.014754 _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] 0.014754 _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] 0.006756 _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 3 NAG X 1 901 901 NAG NAG . E 4 HOH X 1 1001 9 HOH HOH . E 4 HOH X 2 1002 1 HOH HOH . E 4 HOH X 3 1003 97 HOH HOH . E 4 HOH X 4 1004 58 HOH HOH . E 4 HOH X 5 1005 25 HOH HOH . E 4 HOH X 6 1006 121 HOH HOH . E 4 HOH X 7 1007 76 HOH HOH . E 4 HOH X 8 1008 129 HOH HOH . E 4 HOH X 9 1009 29 HOH HOH . E 4 HOH X 10 1010 109 HOH HOH . E 4 HOH X 11 1011 4 HOH HOH . E 4 HOH X 12 1012 41 HOH HOH . E 4 HOH X 13 1013 30 HOH HOH . E 4 HOH X 14 1014 34 HOH HOH . E 4 HOH X 15 1015 74 HOH HOH . E 4 HOH X 16 1016 102 HOH HOH . E 4 HOH X 17 1017 83 HOH HOH . E 4 HOH X 18 1018 88 HOH HOH . E 4 HOH X 19 1019 56 HOH HOH . E 4 HOH X 20 1020 40 HOH HOH . E 4 HOH X 21 1021 93 HOH HOH . E 4 HOH X 22 1022 101 HOH HOH . E 4 HOH X 23 1023 2 HOH HOH . E 4 HOH X 24 1024 22 HOH HOH . E 4 HOH X 25 1025 71 HOH HOH . E 4 HOH X 26 1026 81 HOH HOH . E 4 HOH X 27 1027 117 HOH HOH . E 4 HOH X 28 1028 59 HOH HOH . E 4 HOH X 29 1029 32 HOH HOH . E 4 HOH X 30 1030 63 HOH HOH . E 4 HOH X 31 1031 116 HOH HOH . E 4 HOH X 32 1032 113 HOH HOH . E 4 HOH X 33 1033 28 HOH HOH . E 4 HOH X 34 1034 72 HOH HOH . E 4 HOH X 35 1035 33 HOH HOH . E 4 HOH X 36 1036 123 HOH HOH . E 4 HOH X 37 1037 128 HOH HOH . E 4 HOH X 38 1038 67 HOH HOH . E 4 HOH X 39 1039 54 HOH HOH . E 4 HOH X 40 1040 20 HOH HOH . F 4 HOH Y 1 1001 100 HOH HOH . F 4 HOH Y 2 1002 11 HOH HOH . F 4 HOH Y 3 1003 69 HOH HOH . F 4 HOH Y 4 1004 13 HOH HOH . F 4 HOH Y 5 1005 70 HOH HOH . F 4 HOH Y 6 1006 26 HOH HOH . F 4 HOH Y 7 1007 3 HOH HOH . F 4 HOH Y 8 1008 19 HOH HOH . F 4 HOH Y 9 1009 38 HOH HOH . F 4 HOH Y 10 1010 15 HOH HOH . F 4 HOH Y 11 1011 21 HOH HOH . F 4 HOH Y 12 1012 53 HOH HOH . F 4 HOH Y 13 1013 89 HOH HOH . F 4 HOH Y 14 1014 55 HOH HOH . F 4 HOH Y 15 1015 6 HOH HOH . F 4 HOH Y 16 1016 18 HOH HOH . F 4 HOH Y 17 1017 47 HOH HOH . F 4 HOH Y 18 1018 8 HOH HOH . F 4 HOH Y 19 1019 78 HOH HOH . F 4 HOH Y 20 1020 24 HOH HOH . F 4 HOH Y 21 1021 136 HOH HOH . F 4 HOH Y 22 1022 16 HOH HOH . F 4 HOH Y 23 1023 39 HOH HOH . F 4 HOH Y 24 1024 36 HOH HOH . F 4 HOH Y 25 1025 7 HOH HOH . F 4 HOH Y 26 1026 57 HOH HOH . F 4 HOH Y 27 1027 45 HOH HOH . F 4 HOH Y 28 1028 85 HOH HOH . F 4 HOH Y 29 1029 132 HOH HOH . F 4 HOH Y 30 1030 10 HOH HOH . F 4 HOH Y 31 1031 68 HOH HOH . F 4 HOH Y 32 1032 98 HOH HOH . F 4 HOH Y 33 1033 66 HOH HOH . F 4 HOH Y 34 1034 64 HOH HOH . F 4 HOH Y 35 1035 31 HOH HOH . F 4 HOH Y 36 1036 51 HOH HOH . F 4 HOH Y 37 1037 75 HOH HOH . F 4 HOH Y 38 1038 112 HOH HOH . F 4 HOH Y 39 1039 115 HOH HOH . F 4 HOH Y 40 1040 107 HOH HOH . F 4 HOH Y 41 1041 46 HOH HOH . F 4 HOH Y 42 1042 50 HOH HOH . F 4 HOH Y 43 1043 49 HOH HOH . F 4 HOH Y 44 1044 118 HOH HOH . F 4 HOH Y 45 1045 52 HOH HOH . F 4 HOH Y 46 1046 60 HOH HOH . F 4 HOH Y 47 1047 77 HOH HOH . F 4 HOH Y 48 1048 42 HOH HOH . F 4 HOH Y 49 1049 125 HOH HOH . F 4 HOH Y 50 1050 124 HOH HOH . F 4 HOH Y 51 1051 5 HOH HOH . # 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 . . . D 3 30.274 -13.155 23.331 1 98.76 ? C1 NAG 901 X 1 HETATM 2 C C2 NAG . . . D 3 29.693 -14.214 24.342 1 100.58 ? C2 NAG 901 X 1 HETATM 3 C C3 NAG . . . D 3 30.166 -15.684 23.998 1 102.04 ? C3 NAG 901 X 1 HETATM 4 C C4 NAG . . . D 3 29.993 -16.059 22.502 1 102.63 ? C4 NAG 901 X 1 HETATM 5 C C5 NAG . . . D 3 30.535 -14.925 21.575 1 101.83 ? C5 NAG 901 X 1 HETATM 6 C C6 NAG . . . D 3 30.201 -15.191 20.076 1 103.09 ? C6 NAG 901 X 1 HETATM 7 C C7 NAG . . . D 3 29.027 -13.222 26.604 1 103.16 ? C7 NAG 901 X 1 HETATM 8 C C8 NAG . . . D 3 29.622 -12.887 27.948 1 103.94 ? C8 NAG 901 X 1 HETATM 9 N N2 NAG . . . D 3 29.958 -13.784 25.733 1 101.63 ? N2 NAG 901 X 1 HETATM 10 O O3 NAG . . . D 3 29.519 -16.722 24.793 1 104.12 ? O3 NAG 901 X 1 HETATM 11 O O4 NAG . . . D 3 30.682 -17.321 22.276 1 105.04 ? O4 NAG 901 X 1 HETATM 12 O O5 NAG . . . D 3 30.071 -13.585 21.966 1 100.12 ? O5 NAG 901 X 1 HETATM 13 O O6 NAG . . . D 3 28.959 -14.595 19.631 1 105.23 ? O6 NAG 901 X 1 HETATM 14 O O7 NAG . . . D 3 27.83 -13.009 26.327 1 105.18 ? O7 NAG 901 X 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #