data_5MYA # _model_server_result.job_id 8g6icKxHWylF-jFCcmjzQA _model_server_result.datetime_utc '2024-11-22 15:20:19' _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 5mya # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":807}' # _entry.id 5MYA # _exptl.entry_id 5MYA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 121.41 _cell.angle_gamma 90 _cell.entry_id 5MYA _cell.length_a 134.16 _cell.length_b 104.69 _cell.length_c 79.52 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MYA _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 G N N ? 5 H N N ? 5 I N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . 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 D 101 NAG 2 n C NAG 2 C 2 NAG D 102 NAG 3 n D NAG 1 D 1 NAG D 201 NAG 3 n D NAG 2 D 2 NAG D 202 NAG 3 n D BMA 3 D 3 BMA D 203 BMA 3 n D MAN 4 D 4 MAN D 204 MAN 4 n E NAG 1 E 1 NAG D 501 NAG 4 n E NAG 2 E 2 NAG D 502 NAG 4 n E BMA 3 E 3 BMA D 503 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 covale ? covale1 A ND2 ASN 45 A ASN 464 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 141 A ASN 560 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 177 A ASN 596 1_555 F C1 NAG . A NAG 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 A ND2 ASN 230 A ASN 649 1_555 G C1 NAG . A NAG 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale5 B ND2 ASN 141 B ASN 560 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale6 B ND2 ASN 177 B ASN 596 1_555 H C1 NAG . B NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale7 B ND2 ASN 230 B ASN 649 1_555 I C1 NAG . B NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale13 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 5MYA _atom_sites.fract_transf_matrix[1][1] 0.007454 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004551 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009552 _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] 0.014734 _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 F 5 NAG A 1 807 301 NAG NAG . G 5 NAG A 1 808 401 NAG NAG . H 5 NAG B 1 804 601 NAG NAG . I 5 NAG B 1 805 701 NAG NAG . J 6 HOH A 1 901 75 HOH HOH . J 6 HOH A 2 902 15 HOH HOH . J 6 HOH A 3 903 23 HOH HOH . J 6 HOH A 4 904 67 HOH HOH . J 6 HOH A 5 905 9 HOH HOH . J 6 HOH A 6 906 29 HOH HOH . J 6 HOH A 7 907 32 HOH HOH . J 6 HOH A 8 908 59 HOH HOH . J 6 HOH A 9 909 14 HOH HOH . J 6 HOH A 10 910 19 HOH HOH . J 6 HOH A 11 911 11 HOH HOH . J 6 HOH A 12 912 17 HOH HOH . J 6 HOH A 13 913 72 HOH HOH . J 6 HOH A 14 914 21 HOH HOH . J 6 HOH A 15 915 51 HOH HOH . J 6 HOH A 16 916 22 HOH HOH . J 6 HOH A 17 917 35 HOH HOH . J 6 HOH A 18 918 16 HOH HOH . J 6 HOH A 19 919 56 HOH HOH . J 6 HOH A 20 920 65 HOH HOH . J 6 HOH A 21 921 12 HOH HOH . J 6 HOH A 22 922 44 HOH HOH . J 6 HOH A 23 923 36 HOH HOH . J 6 HOH A 24 924 49 HOH HOH . J 6 HOH A 25 925 31 HOH HOH . J 6 HOH A 26 926 39 HOH HOH . J 6 HOH A 27 927 41 HOH HOH . J 6 HOH A 28 928 71 HOH HOH . J 6 HOH A 29 929 10 HOH HOH . J 6 HOH A 30 930 18 HOH HOH . J 6 HOH A 31 931 27 HOH HOH . J 6 HOH A 32 932 48 HOH HOH . J 6 HOH A 33 933 73 HOH HOH . J 6 HOH A 34 934 37 HOH HOH . J 6 HOH A 35 935 68 HOH HOH . J 6 HOH A 36 936 61 HOH HOH . J 6 HOH A 37 937 70 HOH HOH . J 6 HOH A 38 938 58 HOH HOH . J 6 HOH A 39 939 74 HOH HOH . J 6 HOH A 40 940 13 HOH HOH . J 6 HOH A 41 941 40 HOH HOH . J 6 HOH A 42 942 57 HOH HOH . J 6 HOH A 43 943 66 HOH HOH . J 6 HOH A 44 944 69 HOH HOH . J 6 HOH A 45 945 50 HOH HOH . J 6 HOH A 46 946 28 HOH HOH . J 6 HOH A 47 947 45 HOH HOH . J 6 HOH A 48 948 52 HOH HOH . K 6 HOH B 1 901 5 HOH HOH . K 6 HOH B 2 902 63 HOH HOH . K 6 HOH B 3 903 62 HOH HOH . K 6 HOH B 4 904 34 HOH HOH . K 6 HOH B 5 905 4 HOH HOH . K 6 HOH B 6 906 2 HOH HOH . K 6 HOH B 7 907 46 HOH HOH . K 6 HOH B 8 908 64 HOH HOH . K 6 HOH B 9 909 55 HOH HOH . K 6 HOH B 10 910 43 HOH HOH . K 6 HOH B 11 911 53 HOH HOH . K 6 HOH B 12 912 1 HOH HOH . K 6 HOH B 13 913 47 HOH HOH . K 6 HOH B 14 914 54 HOH HOH . K 6 HOH B 15 915 3 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 . . . F 5 65.635 -28.598 -19.124 1 149.13 ? C1 NAG 807 A 1 HETATM 2 C C2 NAG . . . F 5 64.995 -29.341 -17.949 1 153.25 ? C2 NAG 807 A 1 HETATM 3 C C3 NAG . . . F 5 65.861 -29.192 -16.702 1 151.19 ? C3 NAG 807 A 1 HETATM 4 C C4 NAG . . . F 5 67.309 -29.586 -16.985 1 152.95 ? C4 NAG 807 A 1 HETATM 5 C C5 NAG . . . F 5 67.839 -28.856 -18.218 1 171.31 ? C5 NAG 807 A 1 HETATM 6 C C6 NAG . . . F 5 69.245 -29.321 -18.58 1 168.59 ? C6 NAG 807 A 1 HETATM 7 C C7 NAG . . . F 5 62.489 -29.445 -17.844 1 152.17 ? C7 NAG 807 A 1 HETATM 8 C C8 NAG . . . F 5 62.451 -30.864 -18.344 1 145.29 ? C8 NAG 807 A 1 HETATM 9 N N2 NAG . . . F 5 63.662 -28.81 -17.684 1 156.81 ? N2 NAG 807 A 1 HETATM 10 O O3 NAG . . . F 5 65.333 -30.005 -15.649 1 150.67 ? O3 NAG 807 A 1 HETATM 11 O O4 NAG . . . F 5 68.124 -29.276 -15.849 1 143.24 ? O4 NAG 807 A 1 HETATM 12 O O5 NAG . . . F 5 66.966 -29.083 -19.33 1 171.62 ? O5 NAG 807 A 1 HETATM 13 O O6 NAG . . . F 5 70.174 -28.878 -17.585 1 161.71 ? O6 NAG 807 A 1 HETATM 14 O O7 NAG . . . F 5 61.446 -28.871 -17.582 1 150.56 ? O7 NAG 807 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #