data_1PU4 # _model_server_result.job_id LVg3wYQ-UA0rs-RiY-qn-A _model_server_result.datetime_utc '2024-11-23 12:43:51' _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 1pu4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":2781}' # _entry.id 1PU4 # _exptl.entry_id 1PU4 _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 2 _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 1PU4 _cell.length_a 225.916 _cell.length_b 225.916 _cell.length_c 218.668 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PU4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _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 ? 3 E N N ? 3 I 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 X 2779 NAG 2 n C NAG 2 C 2 NAG X 2780 NAG 2 n D NAG 1 D 1 NAG Y 2779 NAG 2 n D NAG 2 D 2 NAG Y 2780 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 198 A CYS 198 1_555 A SG CYS 199 A CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? disulf ? disulf2 A SG CYS 404 A CYS 404 1_555 A SG CYS 430 A CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf3 A SG CYS 734 A CYS 734 1_555 A SG CYS 741 A CYS 741 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf4 A SG CYS 748 A CYS 748 1_555 B SG CYS 748 B CYS 748 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? disulf ? disulf5 B SG CYS 198 B CYS 198 1_555 B SG CYS 199 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 B SG CYS 404 B CYS 404 1_555 B SG CYS 430 B CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf7 B SG CYS 734 B CYS 734 1_555 B SG CYS 741 B CYS 741 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? covale ? covale1 A ND2 ASN 137 A ASN 137 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 232 A ASN 232 1_555 E C1 NAG . A NAG 2781 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale3 A C ASN 470 A ASN 470 1_555 A N TPQ 471 A TPQ 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale4 A C TPQ 471 A TPQ 471 1_555 A N ASP 472 A ASP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale5 B ND2 ASN 137 B ASN 137 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale6 B ND2 ASN 232 B ASN 232 1_555 I C1 NAG . B NAG 2781 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale7 B C ASN 470 B ASN 470 1_555 B N TPQ 471 B TPQ 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale8 B C TPQ 471 B TPQ 471 1_555 B N ASP 472 B ASP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? metalc ? metalc1 A O4 TPQ 471 A TPQ 471 1_555 F CU CU . A CU 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc2 A NE2 HIS 520 A HIS 520 1_555 F CU CU . A CU 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc3 A NE2 HIS 522 A HIS 522 1_555 F CU CU . A CU 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc4 A OD1 ASP 529 A ASP 529 1_555 G CA CA . A CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc5 A O LEU 530 A LEU 530 1_555 G CA CA . A CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc6 A OD1 ASP 531 A ASP 531 1_555 G CA CA . A CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc7 A OE2 GLU 572 A GLU 572 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? metalc ? metalc8 A OE1 GLU 572 A GLU 572 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc9 A NZ LYS 638 A LYS 638 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? metalc ? metalc10 A O PHE 663 A PHE 663 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc11 A OD1 ASN 665 A ASN 665 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc12 A OE1 GLU 667 A GLU 667 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc13 A OD1 ASP 673 A ASP 673 1_555 G CA CA . A CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc14 A O LEU 674 A LEU 674 1_555 G CA CA . A CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc15 A ND1 HIS 684 A HIS 684 1_555 F CU CU . A CU 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc16 B O4 TPQ 471 B TPQ 471 1_555 J CU CU . B CU 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc17 B NE2 HIS 520 B HIS 520 1_555 J CU CU . B CU 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc18 B NE2 HIS 522 B HIS 522 1_555 J CU CU . B CU 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc19 B OD1 ASP 529 B ASP 529 1_555 K CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc20 B O LEU 530 B LEU 530 1_555 K CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc21 B OD1 ASP 531 B ASP 531 1_555 K CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc22 B OE2 GLU 572 B GLU 572 1_555 L CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc23 B OE1 GLU 572 B GLU 572 1_555 L CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.015 ? metalc ? metalc24 B NZ LYS 638 B LYS 638 1_555 L CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.326 ? metalc ? metalc25 B O PHE 663 B PHE 663 1_555 L CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc26 B OD1 ASN 665 B ASN 665 1_555 L CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc27 B OE1 GLU 667 B GLU 667 1_555 L CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc28 B OD1 ASP 673 B ASP 673 1_555 K CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc29 B O LEU 674 B LEU 674 1_555 K CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc30 B N LEU 674 B LEU 674 1_555 K CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.394 ? metalc ? metalc31 B ND1 HIS 684 B HIS 684 1_555 J CU CU . B CU 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 1PU4 _atom_sites.fract_transf_matrix[1][1] 0.004426 _atom_sites.fract_transf_matrix[1][2] 0.002556 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005111 _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] 0.004573 _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 E 3 NAG A 1 2781 2781 NAG NAG . F 4 CU A 1 801 801 CU CU . G 5 CA A 1 802 802 CA CA . H 5 CA A 1 803 803 CA CA . I 3 NAG B 1 2781 2781 NAG NAG . J 4 CU B 1 801 801 CU CU . K 5 CA B 1 802 802 CA CA . L 5 CA B 1 803 803 CA CA . # 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 3 75.789 123.335 -7.02 1 49.26 ? C1 NAG 2781 B 1 HETATM 2 C C2 NAG . . . I 3 76.584 123.541 -8.335 1 51.81 ? C2 NAG 2781 B 1 HETATM 3 C C3 NAG . . . I 3 75.626 124.126 -9.407 1 53.14 ? C3 NAG 2781 B 1 HETATM 4 C C4 NAG . . . I 3 74.473 123.105 -9.613 1 53.31 ? C4 NAG 2781 B 1 HETATM 5 C C5 NAG . . . I 3 73.748 122.884 -8.268 1 52.53 ? C5 NAG 2781 B 1 HETATM 6 C C6 NAG . . . I 3 72.549 121.938 -8.438 1 52.68 ? C6 NAG 2781 B 1 HETATM 7 C C7 NAG . . . I 3 78.084 125.387 -7.526 1 49.55 ? C7 NAG 2781 B 1 HETATM 8 C C8 NAG . . . I 3 79.35 125.426 -6.683 1 48.63 ? C8 NAG 2781 B 1 HETATM 9 N N2 NAG . . . I 3 77.879 124.234 -8.169 1 50.69 ? N2 NAG 2781 B 1 HETATM 10 O O3 NAG . . . I 3 76.277 124.469 -10.62 1 53.63 ? O3 NAG 2781 B 1 HETATM 11 O O4 NAG . . . I 3 73.549 123.446 -10.644 1 52.91 ? O4 NAG 2781 B 1 HETATM 12 O O5 NAG . . . I 3 74.661 122.459 -7.236 1 50.74 ? O5 NAG 2781 B 1 HETATM 13 O O6 NAG . . . I 3 72.399 121.089 -7.316 1 52.82 ? O6 NAG 2781 B 1 HETATM 14 O O7 NAG . . . I 3 77.303 126.347 -7.646 1 47.26 ? O7 NAG 2781 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #