data_5YKC # _model_server_result.job_id tNgP8wc5-BLd4BeojN66LQ _model_server_result.datetime_utc '2024-11-26 12:07:52' _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 5ykc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":605}' # _entry.id 5YKC # _exptl.entry_id 5YKC _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 12 _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 5YKC _cell.length_a 110.424 _cell.length_b 220.103 _cell.length_c 186.508 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YKC _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,M,N,O,P,Q _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 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P 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 D NAG 1 D 1 NAG A 710 NAG 2 n D NAG 2 D 2 NAG A 711 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 45 A CYS 7 1_555 A SG CYS 504 A CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 96 A CYS 58 1_555 A SG CYS 108 A CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf3 A SG CYS 319 A CYS 281 1_555 A SG CYS 343 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf4 B SG CYS 45 B CYS 7 1_555 B SG CYS 504 B CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 B SG CYS 83 B CYS 45 1_555 B SG CYS 315 B CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf6 B SG CYS 96 B CYS 58 1_555 B SG CYS 108 B CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 319 B CYS 281 1_555 B SG CYS 343 B CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf8 C SG CYS 45 C CYS 7 1_555 C SG CYS 504 C CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? disulf ? disulf9 C SG CYS 83 C CYS 45 1_555 C SG CYS 315 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf10 C SG CYS 96 C CYS 58 1_555 C SG CYS 108 C CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf11 C SG CYS 319 C CYS 281 1_555 C SG CYS 343 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 64 A ASN 26 1_555 G C1 NAG . A NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.516 ? covale ? covale2 A ND2 ASN 95 A ASN 57 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale3 A ND2 ASN 206 A ASN 168 1_555 E C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 A ND2 ASN 327 A ASN 289 1_555 F C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale5 B ND2 ASN 64 B ASN 26 1_555 H C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 B ND2 ASN 95 B ASN 57 1_555 J C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale7 B ND2 ASN 206 B ASN 168 1_555 K C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.37 ? covale ? covale8 B ND2 ASN 277 B ASN 239 1_555 I C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale9 B ND2 ASN 327 B ASN 289 1_555 L C1 NAG . B NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 C ND2 ASN 52 C ASN 14 1_555 O C1 NAG . C NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.713 ? covale ? covale11 C ND2 ASN 64 C ASN 26 1_555 N C1 NAG . C NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale12 C ND2 ASN 95 C ASN 57 1_555 M C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? covale ? covale13 C ND2 ASN 206 C ASN 168 1_555 P C1 NAG . C NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale14 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? # _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 5YKC _atom_sites.fract_transf_matrix[1][1] 0.009056 _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] 0.004543 _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] 0.005362 _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 1 601 510 NAG NAG . F 3 NAG A 1 602 610 NAG NAG . G 3 NAG A 1 605 810 NAG NAG . H 3 NAG B 1 601 510 NAG NAG . I 3 NAG B 1 602 610 NAG NAG . J 3 NAG B 1 603 710 NAG NAG . K 3 NAG B 1 604 711 NAG NAG . L 3 NAG B 1 605 810 NAG NAG . M 3 NAG C 1 601 510 NAG NAG . N 3 NAG C 1 602 610 NAG NAG . O 3 NAG C 1 603 710 NAG NAG . P 3 NAG C 1 604 711 NAG NAG . Q 4 HOH A 1 701 4 HOH HOH . Q 4 HOH A 2 702 2 HOH HOH . Q 4 HOH A 3 703 3 HOH HOH . Q 4 HOH A 4 704 1 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 . . . L 3 -19.53 -35.085 -7.176 1 94.86 ? C1 NAG 605 B 1 HETATM 2 C C2 NAG . . . L 3 -20.908 -35.057 -7.869 1 99.15 ? C2 NAG 605 B 1 HETATM 3 C C3 NAG . . . L 3 -20.78 -34.631 -9.337 1 104.15 ? C3 NAG 605 B 1 HETATM 4 C C4 NAG . . . L 3 -19.971 -33.346 -9.459 1 110.55 ? C4 NAG 605 B 1 HETATM 5 C C5 NAG . . . L 3 -18.628 -33.538 -8.763 1 103.77 ? C5 NAG 605 B 1 HETATM 6 C C6 NAG . . . L 3 -17.74 -32.32 -8.796 1 97.99 ? C6 NAG 605 B 1 HETATM 7 C C7 NAG . . . L 3 -22.86 -36.519 -7.554 1 88.81 ? C7 NAG 605 B 1 HETATM 8 C C8 NAG . . . L 3 -23.339 -37.935 -7.46 1 74.21 ? C8 NAG 605 B 1 HETATM 9 N N2 NAG . . . L 3 -21.55 -36.359 -7.768 1 94.99 ? N2 NAG 605 B 1 HETATM 10 O O3 NAG . . . L 3 -22.082 -34.437 -9.879 1 100.39 ? O3 NAG 605 B 1 HETATM 11 O O4 NAG . . . L 3 -19.782 -32.989 -10.825 1 117.27 ? O4 NAG 605 B 1 HETATM 12 O O5 NAG . . . L 3 -18.857 -33.836 -7.379 1 101.36 ? O5 NAG 605 B 1 HETATM 13 O O6 NAG . . . L 3 -16.817 -32.375 -7.716 1 82.61 ? O6 NAG 605 B 1 HETATM 14 O O7 NAG . . . L 3 -23.624 -35.561 -7.442 1 98.14 ? O7 NAG 605 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #