data_1N8Y # _model_server_result.job_id bHwjstEvn0r44u31rwI9pQ _model_server_result.datetime_utc '2024-11-22 06:54:58' _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 1n8y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":766}' # _entry.id 1N8Y # _exptl.entry_id 1N8Y _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 1N8Y _cell.length_a 130.87 _cell.length_b 116.4 _cell.length_c 55.37 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1N8Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _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 B NAG 1 A 1 NAG D 238 NAG 2 n B NAG 2 A 2 NAG D 238 NAG 2 n C NAG 1 B 1 NAG D 46 NAG 2 n C NAG 2 B 2 NAG D 46 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 4 C CYS 4 1_555 A SG CYS 31 C CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 141 C CYS 141 1_555 A SG CYS 171 C CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 A SG CYS 174 C CYS 174 1_555 A SG CYS 183 C CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 A SG CYS 178 C CYS 178 1_555 A SG CYS 191 C CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf5 A SG CYS 199 C CYS 199 1_555 A SG CYS 206 C CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 A SG CYS 203 C CYS 203 1_555 A SG CYS 214 C CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf7 A SG CYS 215 C CYS 215 1_555 A SG CYS 223 C CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 A SG CYS 219 C CYS 219 1_555 A SG CYS 231 C CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf9 A SG CYS 234 C CYS 234 1_555 A SG CYS 243 C CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf10 A SG CYS 247 C CYS 247 1_555 A SG CYS 274 C CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf11 A SG CYS 278 C CYS 278 1_555 A SG CYS 290 C CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf12 A SG CYS 294 C CYS 294 1_555 A SG CYS 310 C CYS 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf13 A SG CYS 313 C CYS 313 1_555 A SG CYS 317 C CYS 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf14 A SG CYS 321 C CYS 321 1_555 A SG CYS 346 C CYS 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf15 A SG CYS 454 C CYS 454 1_555 A SG CYS 483 C CYS 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? disulf ? disulf16 A SG CYS 490 C CYS 490 1_555 A SG CYS 499 C CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf17 A SG CYS 494 C CYS 494 1_555 A SG CYS 507 C CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf18 A SG CYS 510 C CYS 510 1_555 A SG CYS 519 C CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf19 A SG CYS 523 C CYS 523 1_555 A SG CYS 539 C CYS 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf20 A SG CYS 542 C CYS 542 1_555 A SG CYS 555 C CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf21 A SG CYS 546 C CYS 546 1_555 A SG CYS 563 C CYS 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf22 A SG CYS 566 C CYS 566 1_555 A SG CYS 575 C CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf23 A SG CYS 579 C CYS 579 1_555 A SG CYS 602 C CYS 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? covale ? covale1 A ND2 ASN 46 C ASN 46 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 A ND2 ASN 166 C ASN 166 1_555 D C1 NAG . C NAG 766 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale3 A ND2 ASN 238 C ASN 238 1_555 B C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 B O4 NAG . A NAG 1 1_555 B C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 1N8Y _atom_sites.fract_transf_matrix[1][1] 0.007641 _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] 0.008591 _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] 0.018061 _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 C 1 766 166 NAG NAG . E 4 HOH C 1 769 1 HOH HOH . E 4 HOH C 2 770 2 HOH HOH . E 4 HOH C 3 771 3 HOH HOH . E 4 HOH C 4 772 4 HOH HOH . E 4 HOH C 5 773 5 HOH HOH . E 4 HOH C 6 774 6 HOH HOH . E 4 HOH C 7 775 7 HOH HOH . E 4 HOH C 8 776 8 HOH HOH . E 4 HOH C 9 777 9 HOH HOH . E 4 HOH C 10 778 10 HOH HOH . E 4 HOH C 11 779 11 HOH HOH . E 4 HOH C 12 780 12 HOH HOH . E 4 HOH C 13 781 13 HOH HOH . E 4 HOH C 14 782 14 HOH HOH . E 4 HOH C 15 783 15 HOH HOH . E 4 HOH C 16 784 16 HOH HOH . E 4 HOH C 17 785 17 HOH HOH . E 4 HOH C 18 786 18 HOH HOH . E 4 HOH C 19 787 19 HOH HOH . E 4 HOH C 20 788 20 HOH HOH . E 4 HOH C 21 789 21 HOH HOH . E 4 HOH C 22 790 22 HOH HOH . E 4 HOH C 23 791 23 HOH HOH . E 4 HOH C 24 792 24 HOH HOH . E 4 HOH C 25 793 25 HOH HOH . E 4 HOH C 26 794 26 HOH HOH . E 4 HOH C 27 795 27 HOH HOH . E 4 HOH C 28 796 28 HOH HOH . E 4 HOH C 29 797 29 HOH HOH . E 4 HOH C 30 798 30 HOH HOH . E 4 HOH C 31 799 31 HOH HOH . E 4 HOH C 32 800 32 HOH HOH . E 4 HOH C 33 801 33 HOH HOH . E 4 HOH C 34 802 34 HOH HOH . E 4 HOH C 35 803 35 HOH HOH . E 4 HOH C 36 804 36 HOH HOH . E 4 HOH C 37 805 37 HOH HOH . E 4 HOH C 38 806 38 HOH HOH . E 4 HOH C 39 807 39 HOH HOH . E 4 HOH C 40 808 40 HOH HOH . E 4 HOH C 41 809 41 HOH HOH . E 4 HOH C 42 810 42 HOH HOH . E 4 HOH C 43 811 43 HOH HOH . E 4 HOH C 44 812 44 HOH HOH . E 4 HOH C 45 813 45 HOH HOH . E 4 HOH C 46 814 46 HOH HOH . E 4 HOH C 47 815 47 HOH HOH . E 4 HOH C 48 816 48 HOH HOH . E 4 HOH C 49 817 49 HOH HOH . E 4 HOH C 50 818 50 HOH HOH . E 4 HOH C 51 819 51 HOH HOH . E 4 HOH C 52 820 52 HOH HOH . E 4 HOH C 53 821 53 HOH HOH . E 4 HOH C 54 822 54 HOH HOH . E 4 HOH C 55 823 55 HOH HOH . E 4 HOH C 56 824 56 HOH HOH . E 4 HOH C 57 825 57 HOH HOH . E 4 HOH C 58 826 58 HOH HOH . E 4 HOH C 59 827 59 HOH HOH . E 4 HOH C 60 828 60 HOH HOH . E 4 HOH C 61 829 61 HOH HOH . E 4 HOH C 62 830 62 HOH HOH . E 4 HOH C 63 831 63 HOH HOH . E 4 HOH C 64 832 64 HOH HOH . E 4 HOH C 65 833 65 HOH HOH . E 4 HOH C 66 834 66 HOH HOH . E 4 HOH C 67 835 67 HOH HOH . E 4 HOH C 68 836 68 HOH HOH . E 4 HOH C 69 837 69 HOH HOH . E 4 HOH C 70 838 70 HOH HOH . E 4 HOH C 71 839 71 HOH HOH . E 4 HOH C 72 840 72 HOH HOH . E 4 HOH C 73 841 73 HOH HOH . E 4 HOH C 74 842 74 HOH HOH . E 4 HOH C 75 843 75 HOH HOH . E 4 HOH C 76 844 76 HOH HOH . E 4 HOH C 77 845 77 HOH HOH . E 4 HOH C 78 846 78 HOH HOH . E 4 HOH C 79 847 79 HOH HOH . E 4 HOH C 80 848 80 HOH HOH . E 4 HOH C 81 849 81 HOH HOH . E 4 HOH C 82 850 82 HOH HOH . E 4 HOH C 83 851 83 HOH HOH . E 4 HOH C 84 852 84 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 -23.145 87.055 78.02 1 65.08 ? C1 NAG 766 C 1 HETATM 2 C C2 NAG . . . D 3 -23.272 87.152 79.559 1 71.96 ? C2 NAG 766 C 1 HETATM 3 C C3 NAG . . . D 3 -24.09 86.005 80.182 1 72.61 ? C3 NAG 766 C 1 HETATM 4 C C4 NAG . . . D 3 -25.474 85.972 79.538 1 74.19 ? C4 NAG 766 C 1 HETATM 5 C C5 NAG . . . D 3 -25.234 85.699 78.033 1 74.07 ? C5 NAG 766 C 1 HETATM 6 C C6 NAG . . . D 3 -26.533 85.535 77.214 1 76.22 ? C6 NAG 766 C 1 HETATM 7 C C7 NAG . . . D 3 -21.717 88.006 81.24 1 77.78 ? C7 NAG 766 C 1 HETATM 8 C C8 NAG . . . D 3 -20.755 89.155 81.099 1 77.41 ? C8 NAG 766 C 1 HETATM 9 N N2 NAG . . . D 3 -21.944 87.264 80.146 1 74.55 ? N2 NAG 766 C 1 HETATM 10 O O3 NAG . . . D 3 -24.209 86.116 81.584 1 73.32 ? O3 NAG 766 C 1 HETATM 11 O O4 NAG . . . D 3 -26.316 85.036 80.21 1 74.39 ? O4 NAG 766 C 1 HETATM 12 O O5 NAG . . . D 3 -24.409 86.725 77.439 1 71.32 ? O5 NAG 766 C 1 HETATM 13 O O6 NAG . . . D 3 -27.124 86.781 76.862 1 76.96 ? O6 NAG 766 C 1 HETATM 14 O O7 NAG . . . D 3 -22.259 87.765 82.332 1 79.97 ? O7 NAG 766 C 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 1096 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 14 #