data_5NX2 # _model_server_result.job_id H8sQYKj7FvOQjZIgdKPc5Q _model_server_result.datetime_utc '2025-01-31 03:38:00' _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 5nx2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":603}' # _entry.id 5NX2 # _exptl.entry_id 5NX2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 120 _cell.entry_id 5NX2 _cell.length_a 94.435 _cell.length_b 94.435 _cell.length_c 163.905 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NX2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 3 n C NAG 1 C 1 NAG A 601 NAG 3 n C NAG 2 C 2 NAG A 602 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 27 A CYS 46 1_555 A SG CYS 52 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 43 A CYS 62 1_555 A SG CYS 85 A CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 66 A CYS 85 1_555 A SG CYS 107 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 A SG CYS 207 A CYS 226 1_555 A SG CYS 277 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 44 A ASN 63 1_555 D C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale2 A ND2 ASN 63 A ASN 82 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B C67 9DK 1 B 9DK 1 1_555 B N 9DQ 2 B 9DQ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale4 B C 9DQ 2 B 9DQ 2 1_555 B N GLY 3 B GLY 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale5 B C THR 4 B THR 4 1_555 B N 9DT 5 B 9DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale6 B C 9DT 5 B 9DT 5 1_555 B N THR 6 B THR 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale7 B C ASP 8 B ASP 8 1_555 B N 9DW 9 B 9DW 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale8 B C 9DW 9 B 9DW 9 1_555 B N90 9DZ 10 B 9DZ 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? # _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 390 n n C1 O1 NAG sing 391 n n C1 O5 NAG sing 392 n n C1 H1 NAG sing 393 n n C2 C3 NAG sing 394 n n C2 N2 NAG sing 395 n n C2 H2 NAG sing 396 n n C3 C4 NAG sing 397 n n C3 O3 NAG sing 398 n n C3 H3 NAG sing 399 n n C4 C5 NAG sing 400 n n C4 O4 NAG sing 401 n n C4 H4 NAG sing 402 n n C5 C6 NAG sing 403 n n C5 O5 NAG sing 404 n n C5 H5 NAG sing 405 n n C6 O6 NAG sing 406 n n C6 H61 NAG sing 407 n n C6 H62 NAG sing 408 n n C7 C8 NAG sing 409 n n C7 N2 NAG sing 410 n n C7 O7 NAG doub 411 n n C8 H81 NAG sing 412 n n C8 H82 NAG sing 413 n n C8 H83 NAG sing 414 n n N2 HN2 NAG sing 415 n n O1 HO1 NAG sing 416 n n O3 HO3 NAG sing 417 n n O4 HO4 NAG sing 418 n n O6 HO6 NAG sing 419 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 5NX2 _atom_sites.fract_transf_matrix[1][1] 0.010589 _atom_sites.fract_transf_matrix[1][2] 0.006114 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012227 _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] 0.006101 _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 4 NAG A 1 603 903 NAG NAG . E 5 SOG A 1 604 1 SOG SOG . F 5 SOG A 1 605 2 SOG SOG . G 5 SOG A 1 606 3 SOG SOG . # 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 4 -3.76 37.404 -35.085 1 228.51 ? C1 NAG 603 A 1 HETATM 2 C C2 NAG . . . D 4 -5.105 38.124 -35.025 1 255.41 ? C2 NAG 603 A 1 HETATM 3 C C3 NAG . . . D 4 -6.083 37.621 -36.014 1 274 ? C3 NAG 603 A 1 HETATM 4 C C4 NAG . . . D 4 -5.443 37.544 -37.396 1 272.84 ? C4 NAG 603 A 1 HETATM 5 C C5 NAG . . . D 4 -4.11 36.803 -37.327 1 263.12 ? C5 NAG 603 A 1 HETATM 6 C C6 NAG . . . D 4 -3.445 36.827 -38.701 1 279.01 ? C6 NAG 603 A 1 HETATM 7 C C7 NAG . . . D 4 -6.877 38.713 -33.34 1 283.56 ? C7 NAG 603 A 1 HETATM 8 C C8 NAG . . . D 4 -7.446 38.606 -31.928 1 295.76 ? C8 NAG 603 A 1 HETATM 9 N N2 NAG . . . D 4 -5.646 38.022 -33.681 1 268.39 ? N2 NAG 603 A 1 HETATM 10 O O3 NAG . . . D 4 -6.437 36.306 -35.688 1 283.64 ? O3 NAG 603 A 1 HETATM 11 O O4 NAG . . . D 4 -6.304 36.87 -38.27 1 280.57 ? O4 NAG 603 A 1 HETATM 12 O O5 NAG . . . D 4 -3.272 37.425 -36.395 1 241.08 ? O5 NAG 603 A 1 HETATM 13 O O6 NAG . . . D 4 -3.158 35.517 -39.104 1 289.77 ? O6 NAG 603 A 1 HETATM 14 O O7 NAG . . . D 4 -7.439 39.359 -34.159 1 289.11 ? O7 NAG 603 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 523 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #