data_1NQ9 # _model_server_result.job_id jFMfJIjwjDhWiKmFvDrWXw _model_server_result.datetime_utc '2024-11-23 13:36:46' _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 1nq9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":801}' # _entry.id 1NQ9 # _exptl.entry_id 1NQ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'NTP is a synthetic pentasaccharide based on the naturally occurring antithrombin-binding sequence of heparin' _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _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 109.54 _cell.angle_gamma 90 _cell.entry_id 1NQ9 _cell.length_a 69.679 _cell.length_b 86.76 _cell.length_c 96.921 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NQ9 _symmetry.cell_setting monoclinic _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,F,H,J 1 1 B,D,E,G,I,K 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 ? 4 H N N ? 4 I N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 Z9K Z9L C1 O1 . O4 HO4 . sing 3 ? 3 3 2 GU6 Z9K C1 O1 . O4 HO4 . sing 4 ? 3 4 3 GU1 GU6 C1 O1 . O4 HO4 . sing 5 ? 3 5 4 Z9H GU1 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 A 1 NAG I 841 NAG 2 n C NAG 2 A 2 NAG I 842 NAG 2 n D NAG 1 B 1 NAG L 841 NAG 2 n D NAG 2 B 2 NAG L 842 NAG 2 n E NAG 1 C 1 NAG L 861 NAG 2 n E NAG 2 C 2 NAG L 862 NAG 3 n F Z9L 1 D 1 Z9L J 901 NTP 3 n F Z9K 2 D 2 Z9K J 901 NTP 3 n F GU6 3 D 3 GU6 J 901 NTP 3 n F GU1 4 D 4 GU1 J 901 NTP 3 n F Z9H 5 D 5 Z9H J 901 NTP 3 n G Z9L 1 E 1 Z9L M 901 NTP 3 n G Z9K 2 E 2 Z9K M 901 NTP 3 n G GU6 3 E 3 GU6 M 901 NTP 3 n G GU1 4 E 4 GU1 M 901 NTP 3 n G Z9H 5 E 5 Z9H M 901 NTP # 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 8 I CYS 8 1_555 A SG CYS 128 I CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 21 I CYS 21 1_555 A SG CYS 95 I CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 247 I CYS 247 1_555 A SG CYS 430 I CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 B SG CYS 8 L CYS 8 1_555 B SG CYS 128 L CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 B SG CYS 21 L CYS 21 1_555 B SG CYS 95 L CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 B SG CYS 247 L CYS 247 1_555 B SG CYS 430 L CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 96 I ASN 96 1_555 H C1 NAG . I NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 155 I ASN 155 1_555 C C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 B ND2 ASN 96 L ASN 96 1_555 I C1 NAG . L NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 B ND2 ASN 155 L ASN 155 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale5 B ND2 ASN 192 L ASN 192 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 C O4 NAG . A NAG 1 1_555 C C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale7 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale8 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale9 F O4 Z9L . D Z9L 1 1_555 F C1 Z9K . D Z9K 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 sing covale ? covale10 F O4 Z9K . D Z9K 2 1_555 F C1 GU6 . D GU6 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 sing covale ? covale11 F O4 GU6 . D GU6 3 1_555 F C1 GU1 . D GU1 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 sing covale ? covale12 F O4 GU1 . D GU1 4 1_555 F C1 Z9H . D Z9H 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 sing covale ? covale13 G O4 Z9L . E Z9L 1 1_555 G C1 Z9K . E Z9K 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 sing covale ? covale14 G O4 Z9K . E Z9K 2 1_555 G C1 GU6 . E GU6 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 sing covale ? covale15 G O4 GU6 . E GU6 3 1_555 G C1 GU1 . E GU1 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 sing covale ? covale16 G O4 GU1 . E GU1 4 1_555 G C1 Z9H . E Z9H 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 sing # _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 302 n n C1 O1 NAG sing 303 n n C1 O5 NAG sing 304 n n C1 H1 NAG sing 305 n n C2 C3 NAG sing 306 n n C2 N2 NAG sing 307 n n C2 H2 NAG sing 308 n n C3 C4 NAG sing 309 n n C3 O3 NAG sing 310 n n C3 H3 NAG sing 311 n n C4 C5 NAG sing 312 n n C4 O4 NAG sing 313 n n C4 H4 NAG sing 314 n n C5 C6 NAG sing 315 n n C5 O5 NAG sing 316 n n C5 H5 NAG sing 317 n n C6 O6 NAG sing 318 n n C6 H61 NAG sing 319 n n C6 H62 NAG sing 320 n n C7 C8 NAG sing 321 n n C7 N2 NAG sing 322 n n C7 O7 NAG doub 323 n n C8 H81 NAG sing 324 n n C8 H82 NAG sing 325 n n C8 H83 NAG sing 326 n n N2 HN2 NAG sing 327 n n O1 HO1 NAG sing 328 n n O3 HO3 NAG sing 329 n n O4 HO4 NAG sing 330 n n O6 HO6 NAG sing 331 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 1NQ9 _atom_sites.fract_transf_matrix[1][1] 0.014352 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005093 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011526 _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] 0.010948 _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 H 4 NAG I 1 801 801 NAG NAG . I 4 NAG L 1 801 801 NAG NAG . J 5 HOH I 1 902 1 HOH HOH . J 5 HOH I 2 903 2 HOH HOH . J 5 HOH I 3 904 3 HOH HOH . J 5 HOH I 4 905 4 HOH HOH . J 5 HOH I 5 906 10 HOH HOH . J 5 HOH I 6 907 18 HOH HOH . J 5 HOH I 7 908 19 HOH HOH . J 5 HOH I 8 909 20 HOH HOH . J 5 HOH I 9 910 21 HOH HOH . J 5 HOH I 10 911 22 HOH HOH . J 5 HOH I 11 912 23 HOH HOH . J 5 HOH I 12 913 24 HOH HOH . J 5 HOH I 13 914 25 HOH HOH . J 5 HOH I 14 915 26 HOH HOH . J 5 HOH I 15 916 27 HOH HOH . J 5 HOH I 16 917 28 HOH HOH . J 5 HOH I 17 918 47 HOH HOH . J 5 HOH I 18 919 48 HOH HOH . J 5 HOH I 19 920 49 HOH HOH . J 5 HOH I 20 921 50 HOH HOH . J 5 HOH I 21 922 51 HOH HOH . J 5 HOH I 22 923 52 HOH HOH . J 5 HOH I 23 924 59 HOH HOH . J 5 HOH I 24 925 60 HOH HOH . J 5 HOH I 25 926 61 HOH HOH . J 5 HOH I 26 927 62 HOH HOH . J 5 HOH I 27 928 63 HOH HOH . J 5 HOH I 28 929 64 HOH HOH . J 5 HOH I 29 930 65 HOH HOH . J 5 HOH I 30 931 66 HOH HOH . J 5 HOH I 31 932 67 HOH HOH . J 5 HOH I 32 933 68 HOH HOH . J 5 HOH I 33 934 69 HOH HOH . J 5 HOH I 34 935 70 HOH HOH . J 5 HOH I 35 936 71 HOH HOH . J 5 HOH I 36 937 72 HOH HOH . K 5 HOH L 1 902 5 HOH HOH . K 5 HOH L 2 903 6 HOH HOH . K 5 HOH L 3 904 7 HOH HOH . K 5 HOH L 4 905 8 HOH HOH . K 5 HOH L 5 906 9 HOH HOH . K 5 HOH L 6 907 11 HOH HOH . K 5 HOH L 7 908 12 HOH HOH . K 5 HOH L 8 909 13 HOH HOH . K 5 HOH L 9 910 14 HOH HOH . K 5 HOH L 10 911 15 HOH HOH . K 5 HOH L 11 912 16 HOH HOH . K 5 HOH L 12 913 17 HOH HOH . K 5 HOH L 13 914 29 HOH HOH . K 5 HOH L 14 915 30 HOH HOH . K 5 HOH L 15 916 31 HOH HOH . K 5 HOH L 16 917 32 HOH HOH . K 5 HOH L 17 918 33 HOH HOH . K 5 HOH L 18 919 34 HOH HOH . K 5 HOH L 19 920 35 HOH HOH . K 5 HOH L 20 921 36 HOH HOH . K 5 HOH L 21 922 37 HOH HOH . K 5 HOH L 22 923 38 HOH HOH . K 5 HOH L 23 924 39 HOH HOH . K 5 HOH L 24 925 40 HOH HOH . K 5 HOH L 25 926 41 HOH HOH . K 5 HOH L 26 927 42 HOH HOH . K 5 HOH L 27 928 43 HOH HOH . K 5 HOH L 28 929 44 HOH HOH . K 5 HOH L 29 930 45 HOH HOH . K 5 HOH L 30 931 46 HOH HOH . K 5 HOH L 31 932 53 HOH HOH . K 5 HOH L 32 933 54 HOH HOH . K 5 HOH L 33 934 55 HOH HOH . K 5 HOH L 34 935 56 HOH HOH . K 5 HOH L 35 936 57 HOH HOH . K 5 HOH L 36 937 58 HOH HOH . K 5 HOH L 37 938 73 HOH HOH . K 5 HOH L 38 939 74 HOH HOH . K 5 HOH L 39 940 75 HOH HOH . K 5 HOH L 40 941 76 HOH HOH . K 5 HOH L 41 942 77 HOH HOH . K 5 HOH L 42 943 78 HOH HOH . K 5 HOH L 43 944 79 HOH HOH . K 5 HOH L 44 945 80 HOH HOH . K 5 HOH L 45 946 81 HOH HOH . K 5 HOH L 46 947 82 HOH HOH . K 5 HOH L 47 948 83 HOH HOH . K 5 HOH L 48 949 84 HOH HOH . K 5 HOH L 49 950 85 HOH HOH . K 5 HOH L 50 951 86 HOH HOH . K 5 HOH L 51 952 87 HOH HOH . K 5 HOH L 52 953 88 HOH HOH . K 5 HOH L 53 954 89 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 -27.223 0.995 31.2 1 66.72 ? C1 NAG 801 L 1 HETATM 2 C C2 NAG . . . I 4 -28.678 1.301 31.581 1 68.44 ? C2 NAG 801 L 1 HETATM 3 C C3 NAG . . . I 4 -29.078 0.441 32.778 1 68.53 ? C3 NAG 801 L 1 HETATM 4 C C4 NAG . . . I 4 -28.881 -1.03 32.421 1 68.73 ? C4 NAG 801 L 1 HETATM 5 C C5 NAG . . . I 4 -27.418 -1.263 32.021 1 68.28 ? C5 NAG 801 L 1 HETATM 6 C C6 NAG . . . I 4 -27.172 -2.7 31.58 1 69.78 ? C6 NAG 801 L 1 HETATM 7 C C7 NAG . . . I 4 -28.896 3.616 30.932 1 70.49 ? C7 NAG 801 L 1 HETATM 8 C C8 NAG . . . I 4 -28.131 4.915 31.148 1 69.66 ? C8 NAG 801 L 1 HETATM 9 N N2 NAG . . . I 4 -28.837 2.709 31.903 1 70.24 ? N2 NAG 801 L 1 HETATM 10 O O3 NAG . . . I 4 -30.433 0.686 33.122 1 67.21 ? O3 NAG 801 L 1 HETATM 11 O O4 NAG . . . I 4 -29.227 -1.848 33.531 1 70.94 ? O4 NAG 801 L 1 HETATM 12 O O5 NAG . . . I 4 -27.065 -0.405 30.908 1 67.62 ? O5 NAG 801 L 1 HETATM 13 O O6 NAG . . . I 4 -25.828 -2.903 31.16 1 71.24 ? O6 NAG 801 L 1 HETATM 14 O O7 NAG . . . I 4 -29.527 3.436 29.888 1 70.36 ? O7 NAG 801 L 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #