data_5EB5 # _model_server_result.job_id PgBo_a-K0PzdUHkxXPwTOQ _model_server_result.datetime_utc '2025-01-11 09:13:12' _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 5eb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":608}' # _entry.id 5EB5 # _exptl.entry_id 5EB5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.01 _cell.angle_gamma 90 _cell.entry_id 5EB5 _cell.length_a 68.364 _cell.length_b 95.161 _cell.length_c 92.19 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EB5 _symmetry.cell_setting ? _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,D,G,H,I,J,K,O 1 1 B,E,F,L,M,N,P 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 ? 4 J N N ? 4 M N 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 C 1 NAG A 600 NAG 2 n C NAG 2 C 2 NAG A 601 NAG 2 n D NAG 1 D 1 NAG A 604 NAG 2 n D NAG 2 D 2 NAG A 605 NAG 2 n E NAG 1 E 1 NAG B 600 NAG 2 n E NAG 2 E 2 NAG B 601 NAG 2 n F NAG 1 F 1 NAG B 602 NAG 2 n F NAG 2 F 2 NAG B 603 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 400 A CYS 400 1_555 A SG CYS 451 A CYS 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf2 B SG CYS 400 B CYS 400 1_555 B SG CYS 451 B CYS 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 118 A ASN 118 1_555 I C1 NAG . A NAG 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 135 A ASN 135 1_555 J C1 NAG . A NAG 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 191 A ASN 191 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 A ND2 ASN 353 A ASN 353 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 A ND2 ASN 393 A ASN 393 1_555 H C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 B ND2 ASN 118 B ASN 118 1_555 M C1 NAG . B NAG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B ND2 ASN 135 B ASN 135 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 B ND2 ASN 191 B ASN 191 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 NAG . F 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 344 n n C1 O1 NAG sing 345 n n C1 O5 NAG sing 346 n n C1 H1 NAG sing 347 n n C2 C3 NAG sing 348 n n C2 N2 NAG sing 349 n n C2 H2 NAG sing 350 n n C3 C4 NAG sing 351 n n C3 O3 NAG sing 352 n n C3 H3 NAG sing 353 n n C4 C5 NAG sing 354 n n C4 O4 NAG sing 355 n n C4 H4 NAG sing 356 n n C5 C6 NAG sing 357 n n C5 O5 NAG sing 358 n n C5 H5 NAG sing 359 n n C6 O6 NAG sing 360 n n C6 H61 NAG sing 361 n n C6 H62 NAG sing 362 n n C7 C8 NAG sing 363 n n C7 N2 NAG sing 364 n n C7 O7 NAG doub 365 n n C8 H81 NAG sing 366 n n C8 H82 NAG sing 367 n n C8 H83 NAG sing 368 n n N2 HN2 NAG sing 369 n n O1 HO1 NAG sing 370 n n O3 HO3 NAG sing 371 n n O4 HO4 NAG sing 372 n n O6 HO6 NAG sing 373 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 5EB5 _atom_sites.fract_transf_matrix[1][1] 0.014628 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000003 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010509 _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] 0.010847 _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 G 3 FAD A 1 601 550 FAD FAD . H 4 NAG A 1 604 603 NAG NAG . I 4 NAG A 1 607 606 NAG NAG . J 4 NAG A 1 608 607 NAG NAG . K 5 010 A 1 609 1000 010 010 . L 3 FAD B 1 601 550 FAD FAD . M 4 NAG B 1 606 604 NAG NAG . N 5 010 B 1 607 1000 010 010 . O 6 HOH A 1 701 195 HOH HOH . O 6 HOH A 2 702 3 HOH HOH . O 6 HOH A 3 703 10 HOH HOH . O 6 HOH A 4 704 174 HOH HOH . O 6 HOH A 5 705 200 HOH HOH . O 6 HOH A 6 706 170 HOH HOH . O 6 HOH A 7 707 202 HOH HOH . O 6 HOH A 8 708 56 HOH HOH . O 6 HOH A 9 709 194 HOH HOH . O 6 HOH A 10 710 203 HOH HOH . O 6 HOH A 11 711 29 HOH HOH . O 6 HOH A 12 712 183 HOH HOH . O 6 HOH A 13 713 36 HOH HOH . O 6 HOH A 14 714 13 HOH HOH . O 6 HOH A 15 715 206 HOH HOH . O 6 HOH A 16 716 158 HOH HOH . O 6 HOH A 17 717 207 HOH HOH . O 6 HOH A 18 718 184 HOH HOH . O 6 HOH A 19 719 180 HOH HOH . O 6 HOH A 20 720 176 HOH HOH . O 6 HOH A 21 721 154 HOH HOH . O 6 HOH A 22 722 173 HOH HOH . O 6 HOH A 23 723 196 HOH HOH . O 6 HOH A 24 724 152 HOH HOH . O 6 HOH A 25 725 204 HOH HOH . O 6 HOH A 26 726 157 HOH HOH . O 6 HOH A 27 727 28 HOH HOH . O 6 HOH A 28 728 187 HOH HOH . O 6 HOH A 29 729 191 HOH HOH . O 6 HOH A 30 730 208 HOH HOH . O 6 HOH A 31 731 21 HOH HOH . O 6 HOH A 32 732 4 HOH HOH . O 6 HOH A 33 733 163 HOH HOH . O 6 HOH A 34 734 153 HOH HOH . O 6 HOH A 35 735 167 HOH HOH . O 6 HOH A 36 736 172 HOH HOH . O 6 HOH A 37 737 215 HOH HOH . O 6 HOH A 38 738 162 HOH HOH . O 6 HOH A 39 739 201 HOH HOH . O 6 HOH A 40 740 190 HOH HOH . O 6 HOH A 41 741 197 HOH HOH . P 6 HOH B 1 701 216 HOH HOH . P 6 HOH B 2 702 213 HOH HOH . P 6 HOH B 3 703 189 HOH HOH . P 6 HOH B 4 704 9 HOH HOH . P 6 HOH B 5 705 182 HOH HOH . P 6 HOH B 6 706 192 HOH HOH . P 6 HOH B 7 707 14 HOH HOH . P 6 HOH B 8 708 219 HOH HOH . P 6 HOH B 9 709 205 HOH HOH . P 6 HOH B 10 710 212 HOH HOH . P 6 HOH B 11 711 164 HOH HOH . P 6 HOH B 12 712 25 HOH HOH . P 6 HOH B 13 713 151 HOH HOH . P 6 HOH B 14 714 186 HOH HOH . P 6 HOH B 15 715 220 HOH HOH . P 6 HOH B 16 716 166 HOH HOH . P 6 HOH B 17 717 222 HOH HOH . P 6 HOH B 18 718 177 HOH HOH . P 6 HOH B 19 719 211 HOH HOH . P 6 HOH B 20 720 179 HOH HOH . P 6 HOH B 21 721 181 HOH HOH . P 6 HOH B 22 722 193 HOH HOH . P 6 HOH B 23 723 150 HOH HOH . P 6 HOH B 24 724 217 HOH HOH . P 6 HOH B 25 725 160 HOH HOH . P 6 HOH B 26 726 225 HOH HOH . P 6 HOH B 27 727 223 HOH HOH . P 6 HOH B 28 728 1 HOH HOH . P 6 HOH B 29 729 148 HOH HOH . P 6 HOH B 30 730 161 HOH HOH . P 6 HOH B 31 731 41 HOH HOH . P 6 HOH B 32 732 45 HOH HOH . P 6 HOH B 33 733 224 HOH HOH . P 6 HOH B 34 734 214 HOH HOH . P 6 HOH B 35 735 199 HOH HOH . P 6 HOH B 36 736 149 HOH HOH . P 6 HOH B 37 737 210 HOH HOH . P 6 HOH B 38 738 218 HOH HOH . P 6 HOH B 39 739 198 HOH HOH . P 6 HOH B 40 740 155 HOH HOH . P 6 HOH B 41 741 171 HOH HOH . P 6 HOH B 42 742 209 HOH HOH . P 6 HOH B 43 743 221 HOH HOH . P 6 HOH B 44 744 156 HOH HOH . P 6 HOH B 45 745 188 HOH HOH . P 6 HOH B 46 746 175 HOH HOH . P 6 HOH B 47 747 168 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 . . . J 4 20.819 -19.808 5.377 1 39.21 ? C1 NAG 608 A 1 HETATM 2 C C2 NAG . . . J 4 20.39 -21.273 5.582 1 39.91 ? C2 NAG 608 A 1 HETATM 3 C C3 NAG . . . J 4 19.193 -21.404 6.536 1 39.76 ? C3 NAG 608 A 1 HETATM 4 C C4 NAG . . . J 4 19.399 -20.607 7.831 1 39.66 ? C4 NAG 608 A 1 HETATM 5 C C5 NAG . . . J 4 19.728 -19.146 7.497 1 39.24 ? C5 NAG 608 A 1 HETATM 6 C C6 NAG . . . J 4 20.041 -18.335 8.75 1 38.82 ? C6 NAG 608 A 1 HETATM 7 C C7 NAG . . . J 4 20.952 -22.605 3.567 1 40.61 ? C7 NAG 608 A 1 HETATM 8 C C8 NAG . . . J 4 20.386 -23.179 2.302 1 40.66 ? C8 NAG 608 A 1 HETATM 9 N N2 NAG . . . J 4 20.077 -21.918 4.314 1 40.31 ? N2 NAG 608 A 1 HETATM 10 O O3 NAG . . . J 4 18.985 -22.785 6.848 1 39.76 ? O3 NAG 608 A 1 HETATM 11 O O4 NAG . . . J 4 18.24 -20.702 8.673 1 39.76 ? O4 NAG 608 A 1 HETATM 12 O O5 NAG . . . J 4 20.868 -19.087 6.622 1 39.23 ? O5 NAG 608 A 1 HETATM 13 O O6 NAG . . . J 4 20.777 -17.154 8.403 1 38.77 ? O6 NAG 608 A 1 HETATM 14 O O7 NAG . . . J 4 22.129 -22.764 3.861 1 40.58 ? O7 NAG 608 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #