data_5Z5K # _model_server_result.job_id RVt3HZiatacW-kv5u3UHUw _model_server_result.datetime_utc '2025-01-25 20:10:28' _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 5z5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":507}' # _entry.id 5Z5K # _exptl.entry_id 5Z5K _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 5Z5K _cell.length_a 108.069 _cell.length_b 108.069 _cell.length_c 130.266 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z5K _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 F _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 439 NAG 3 n C NAG 2 C 2 NAG A 440 NAG 3 n D NAG 1 D 1 NAG A 442 NAG 3 n D NAG 2 D 2 NAG A 443 NAG 3 n E NAG 1 E 1 NAG A 445 NAG 3 n E NAG 2 E 2 NAG A 446 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 23 A CYS 61 1_555 A SG CYS 79 A CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 123 A CYS 161 1_555 A SG CYS 174 A CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 223 A CYS 261 1_555 A SG CYS 272 A CYS 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 314 A CYS 352 1_555 A SG CYS 362 A CYS 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 B SG CYS 4 B CYS 267 1_555 B SG CYS 16 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 10 B CYS 273 1_555 B SG CYS 23 B CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 15 B CYS 278 1_555 B SG CYS 38 B CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 34 B CYS 297 1_555 B SG CYS 46 B CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 40 B CYS 303 1_555 B SG CYS 63 B CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 22 A ASN 60 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale2 A ND2 ASN 56 A ASN 94 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale3 A ND2 ASN 261 A ASN 299 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale4 A ND2 ASN 280 A ASN 318 1_555 F C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _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 5Z5K _atom_sites.fract_transf_matrix[1][1] 0.009253 _atom_sites.fract_transf_matrix[1][2] 0.005342 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010685 _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] 0.007677 _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 F 4 NAG A 1 507 447 NAG NAG . G 5 HOH A 1 601 21 HOH HOH . G 5 HOH A 2 602 9 HOH HOH . G 5 HOH A 3 603 23 HOH HOH . G 5 HOH A 4 604 18 HOH HOH . G 5 HOH A 5 605 7 HOH HOH . G 5 HOH A 6 606 5 HOH HOH . G 5 HOH A 7 607 16 HOH HOH . G 5 HOH A 8 608 10 HOH HOH . G 5 HOH A 9 609 28 HOH HOH . G 5 HOH A 10 610 22 HOH HOH . G 5 HOH A 11 611 20 HOH HOH . G 5 HOH A 12 612 13 HOH HOH . G 5 HOH A 13 613 6 HOH HOH . G 5 HOH A 14 614 4 HOH HOH . G 5 HOH A 15 615 26 HOH HOH . G 5 HOH A 16 616 3 HOH HOH . G 5 HOH A 17 617 1 HOH HOH . G 5 HOH A 18 618 32 HOH HOH . G 5 HOH A 19 619 12 HOH HOH . G 5 HOH A 20 620 25 HOH HOH . G 5 HOH A 21 621 30 HOH HOH . G 5 HOH A 22 622 2 HOH HOH . G 5 HOH A 23 623 27 HOH HOH . G 5 HOH A 24 624 8 HOH HOH . G 5 HOH A 25 625 31 HOH HOH . G 5 HOH A 26 626 19 HOH HOH . G 5 HOH A 27 627 24 HOH HOH . G 5 HOH A 28 628 15 HOH HOH . G 5 HOH A 29 629 29 HOH HOH . G 5 HOH A 30 630 11 HOH HOH . G 5 HOH A 31 631 17 HOH HOH . G 5 HOH A 32 632 14 HOH HOH . G 5 HOH A 33 633 33 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 . . . F 4 9.464 127.241 -39.409 1 135.03 ? C1 NAG 507 A 1 HETATM 2 C C2 NAG . . . F 4 8.49 126.598 -38.426 1 141.59 ? C2 NAG 507 A 1 HETATM 3 C C3 NAG . . . F 4 9.104 125.335 -37.83 1 148.54 ? C3 NAG 507 A 1 HETATM 4 C C4 NAG . . . F 4 9.541 124.388 -38.94 1 149.63 ? C4 NAG 507 A 1 HETATM 5 C C5 NAG . . . F 4 10.465 125.111 -39.918 1 139.03 ? C5 NAG 507 A 1 HETATM 6 C C6 NAG . . . F 4 10.831 124.266 -41.116 1 135.15 ? C6 NAG 507 A 1 HETATM 7 C C7 NAG . . . F 4 6.92 128.137 -37.337 1 138.18 ? C7 NAG 507 A 1 HETATM 8 C C8 NAG . . . F 4 6.691 129.06 -36.179 1 135.84 ? C8 NAG 507 A 1 HETATM 9 N N2 NAG . . . F 4 8.11 127.527 -37.375 1 139.11 ? N2 NAG 507 A 1 HETATM 10 O O3 NAG . . . F 4 8.152 124.697 -36.987 1 155.96 ? O3 NAG 507 A 1 HETATM 11 O O4 NAG . . . F 4 10.222 123.269 -38.386 1 154.63 ? O4 NAG 507 A 1 HETATM 12 O O5 NAG . . . F 4 9.822 126.291 -40.424 1 133.62 ? O5 NAG 507 A 1 HETATM 13 O O6 NAG . . . F 4 9.869 123.246 -41.345 1 136.01 ? O6 NAG 507 A 1 HETATM 14 O O7 NAG . . . F 4 6.067 127.951 -38.2 1 138.46 ? O7 NAG 507 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #