data_6OMO # _model_server_result.job_id NcGi_Dwqz4N7opeTkzb9LQ _model_server_result.datetime_utc '2024-11-04 22:22:49' _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 6omo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1006}' # _entry.id 6OMO # _exptl.entry_id 6OMO _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 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 6OMO _cell.length_a 97.398 _cell.length_b 97.398 _cell.length_c 85.644 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6OMO _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,G,H,I,J,K,L,M,N _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 4 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A 1 NAG J 901 NAG 2 n C NAG 2 A 2 NAG J 902 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 I CYS 38 1_555 A SG CYS 69 I CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 32 I CYS 67 1_555 A SG CYS 101 I CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf3 A SG CYS 36 I CYS 71 1_555 A SG CYS 103 I CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 A SG CYS 68 I CYS 103 1_555 B SG CYS 68 J CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 B SG CYS 3 J CYS 38 1_555 B SG CYS 69 J CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf6 B SG CYS 32 J CYS 67 1_555 B SG CYS 101 J CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf7 B SG CYS 36 J CYS 71 1_555 B SG CYS 103 J CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 45 I ASN 80 1_555 I C1 NAG . I NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.507 ? covale ? covale2 B ND2 ASN 45 J ASN 80 1_555 C C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale3 C O4 NAG . A NAG 1 1_555 C C1 NAG . A 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 248 n n C1 O1 NAG sing 249 n n C1 O5 NAG sing 250 n n C1 H1 NAG sing 251 n n C2 C3 NAG sing 252 n n C2 N2 NAG sing 253 n n C2 H2 NAG sing 254 n n C3 C4 NAG sing 255 n n C3 O3 NAG sing 256 n n C3 H3 NAG sing 257 n n C4 C5 NAG sing 258 n n C4 O4 NAG sing 259 n n C4 H4 NAG sing 260 n n C5 C6 NAG sing 261 n n C5 O5 NAG sing 262 n n C5 H5 NAG sing 263 n n C6 O6 NAG sing 264 n n C6 H61 NAG sing 265 n n C6 H62 NAG sing 266 n n C7 C8 NAG sing 267 n n C7 N2 NAG sing 268 n n C7 O7 NAG doub 269 n n C8 H81 NAG sing 270 n n C8 H82 NAG sing 271 n n C8 H83 NAG sing 272 n n N2 HN2 NAG sing 273 n n O1 HO1 NAG sing 274 n n O3 HO3 NAG sing 275 n n O4 HO4 NAG sing 276 n n O6 HO6 NAG sing 277 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 6OMO _atom_sites.fract_transf_matrix[1][1] 0.010267 _atom_sites.fract_transf_matrix[1][2] 0.005928 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011855 _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] 0.011676 _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 IPA I 1 1001 401 IPA IPA . E 3 IPA I 1 1002 402 IPA IPA . F 3 IPA I 1 1003 404 IPA IPA . G 3 IPA I 1 1004 405 IPA IPA . H 3 IPA I 1 1005 406 IPA IPA . I 4 NAG I 1 1006 901 NAG NAG . J 3 IPA J 1 1001 403 IPA IPA . K 5 PEG J 1 1002 501 PEG PEG . L 5 PEG J 1 1003 502 PEG PEG . M 6 HOH I 1 1101 13 HOH HOH . M 6 HOH I 2 1102 31 HOH HOH . M 6 HOH I 3 1103 65 HOH HOH . M 6 HOH I 4 1104 8 HOH HOH . M 6 HOH I 5 1105 16 HOH HOH . M 6 HOH I 6 1106 9 HOH HOH . M 6 HOH I 7 1107 33 HOH HOH . M 6 HOH I 8 1108 17 HOH HOH . M 6 HOH I 9 1109 46 HOH HOH . M 6 HOH I 10 1110 50 HOH HOH . M 6 HOH I 11 1111 70 HOH HOH . M 6 HOH I 12 1112 40 HOH HOH . M 6 HOH I 13 1113 15 HOH HOH . M 6 HOH I 14 1114 38 HOH HOH . M 6 HOH I 15 1115 55 HOH HOH . M 6 HOH I 16 1116 45 HOH HOH . M 6 HOH I 17 1117 22 HOH HOH . M 6 HOH I 18 1118 39 HOH HOH . M 6 HOH I 19 1119 41 HOH HOH . M 6 HOH I 20 1120 61 HOH HOH . M 6 HOH I 21 1121 62 HOH HOH . N 6 HOH J 1 1101 51 HOH HOH . N 6 HOH J 2 1102 52 HOH HOH . N 6 HOH J 3 1103 49 HOH HOH . N 6 HOH J 4 1104 20 HOH HOH . N 6 HOH J 5 1105 28 HOH HOH . N 6 HOH J 6 1106 6 HOH HOH . N 6 HOH J 7 1107 30 HOH HOH . N 6 HOH J 8 1108 26 HOH HOH . N 6 HOH J 9 1109 19 HOH HOH . N 6 HOH J 10 1110 21 HOH HOH . N 6 HOH J 11 1111 34 HOH HOH . N 6 HOH J 12 1112 29 HOH HOH . N 6 HOH J 13 1113 35 HOH HOH . N 6 HOH J 14 1114 58 HOH HOH . N 6 HOH J 15 1115 3 HOH HOH . N 6 HOH J 16 1116 73 HOH HOH . N 6 HOH J 17 1117 47 HOH HOH . N 6 HOH J 18 1118 77 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 . . . I 4 51.598 10.655 16.376 1 106.49 ? C1 NAG 1006 I 1 HETATM 2 C C2 NAG . . . I 4 52.097 10.658 14.878 1 108.25 ? C2 NAG 1006 I 1 HETATM 3 C C3 NAG . . . I 4 51.613 11.924 14.078 1 109.66 ? C3 NAG 1006 I 1 HETATM 4 C C4 NAG . . . I 4 50.077 12.191 14.262 1 110.16 ? C4 NAG 1006 I 1 HETATM 5 C C5 NAG . . . I 4 49.67 12.333 15.771 1 109.33 ? C5 NAG 1006 I 1 HETATM 6 C C6 NAG . . . I 4 48.132 12.605 16.029 1 110.35 ? C6 NAG 1006 I 1 HETATM 7 C C7 NAG . . . I 4 54.255 9.308 14.556 1 110.83 ? C7 NAG 1006 I 1 HETATM 8 C C8 NAG . . . I 4 55.76 9.443 14.672 1 111.61 ? C8 NAG 1006 I 1 HETATM 9 N N2 NAG . . . I 4 53.57 10.467 14.883 1 109.3 ? N2 NAG 1006 I 1 HETATM 10 O O3 NAG . . . I 4 51.96 11.855 12.655 1 111.75 ? O3 NAG 1006 I 1 HETATM 11 O O4 NAG . . . I 4 49.682 13.317 13.428 1 112.46 ? O4 NAG 1006 I 1 HETATM 12 O O5 NAG . . . I 4 50.311 11.351 16.705 1 107.77 ? O5 NAG 1006 I 1 HETATM 13 O O6 NAG . . . I 4 47.195 11.516 15.902 1 111.76 ? O6 NAG 1006 I 1 HETATM 14 O O7 NAG . . . I 4 53.695 8.258 14.201 1 112.95 ? O7 NAG 1006 I 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #