data_5F4P # _model_server_result.job_id S-9tmmpwO1qxHVSG1Yqvzg _model_server_result.datetime_utc '2024-11-29 10:29:06' _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 5f4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":502}' # _entry.id 5F4P # _exptl.entry_id 5F4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _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 5F4P _cell.length_a 67.378 _cell.length_b 127.517 _cell.length_c 192.945 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F4P _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 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,M,N,O,P,Q,R _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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N # 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 6 D CYS 54 1_555 A SG CYS 26 D CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 71 D CYS 119 1_555 A SG CYS 84 D CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 97 D CYS 218 1_555 A SG CYS 126 D CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 107 D CYS 228 1_555 A SG CYS 118 D CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 175 D CYS 296 1_555 A SG CYS 194 D CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 240 D CYS 378 1_555 A SG CYS 304 D CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 A SG CYS 247 D CYS 385 1_555 A SG CYS 277 D CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 6 A CYS 54 1_555 B SG CYS 26 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 B SG CYS 71 A CYS 119 1_555 B SG CYS 84 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 B SG CYS 97 A CYS 218 1_555 B SG CYS 126 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 B SG CYS 107 A CYS 228 1_555 B SG CYS 118 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 B SG CYS 175 A CYS 296 1_555 B SG CYS 194 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf13 B SG CYS 240 A CYS 378 1_555 B SG CYS 304 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf14 B SG CYS 247 A CYS 385 1_555 B SG CYS 277 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _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 294 n n C1 O1 NAG sing 295 n n C1 O5 NAG sing 296 n n C1 H1 NAG sing 297 n n C2 C3 NAG sing 298 n n C2 N2 NAG sing 299 n n C2 H2 NAG sing 300 n n C3 C4 NAG sing 301 n n C3 O3 NAG sing 302 n n C3 H3 NAG sing 303 n n C4 C5 NAG sing 304 n n C4 O4 NAG sing 305 n n C4 H4 NAG sing 306 n n C5 C6 NAG sing 307 n n C5 O5 NAG sing 308 n n C5 H5 NAG sing 309 n n C6 O6 NAG sing 310 n n C6 H61 NAG sing 311 n n C6 H62 NAG sing 312 n n C7 C8 NAG sing 313 n n C7 N2 NAG sing 314 n n C7 O7 NAG doub 315 n n C8 H81 NAG sing 316 n n C8 H82 NAG sing 317 n n C8 H83 NAG sing 318 n n N2 HN2 NAG sing 319 n n O1 HO1 NAG sing 320 n n O3 HO3 NAG sing 321 n n O4 HO4 NAG sing 322 n n O6 HO6 NAG sing 323 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 5F4P _atom_sites.fract_transf_matrix[1][1] 0.014842 _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] 0.007842 _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] 0.005183 _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 C 2 NAG D 1 501 503 NAG NAG . D 2 NAG D 1 502 504 NAG NAG . E 2 NAG D 1 503 505 NAG NAG . F 2 NAG D 1 504 506 NAG NAG . G 2 NAG D 1 505 507 NAG NAG . H 2 NAG D 1 506 508 NAG NAG . I 3 5VG D 1 507 501 5VG LIG . J 3 5VG A 1 501 501 5VG LIG . K 2 NAG A 1 502 503 NAG NAG . L 2 NAG A 1 503 504 NAG NAG . M 2 NAG A 1 504 505 NAG NAG . N 2 NAG A 1 505 506 NAG NAG . O 2 NAG A 1 506 507 NAG NAG . P 2 NAG A 1 507 508 NAG NAG . Q 4 HOH D 1 601 6 HOH HOH . Q 4 HOH D 2 602 8 HOH HOH . Q 4 HOH D 3 603 9 HOH HOH . Q 4 HOH D 4 604 12 HOH HOH . Q 4 HOH D 5 605 10 HOH HOH . Q 4 HOH D 6 606 2 HOH HOH . R 4 HOH A 1 601 11 HOH HOH . R 4 HOH A 2 602 13 HOH HOH . R 4 HOH A 3 603 1 HOH HOH . R 4 HOH A 4 604 7 HOH HOH . R 4 HOH A 5 605 5 HOH HOH . R 4 HOH A 6 606 4 HOH HOH . R 4 HOH A 7 607 3 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 . . . K 2 -2.521 -5.614 40.56 1 103.95 ? C1 NAG 502 A 1 HETATM 2 C C2 NAG . . . K 2 -2.996 -4.204 40.939 1 106.51 ? C2 NAG 502 A 1 HETATM 3 C C3 NAG . . . K 2 -1.896 -3.168 40.681 1 106.21 ? C3 NAG 502 A 1 HETATM 4 C C4 NAG . . . K 2 -0.569 -3.615 41.285 1 110.15 ? C4 NAG 502 A 1 HETATM 5 C C5 NAG . . . K 2 -0.24 -5.021 40.813 1 104.07 ? C5 NAG 502 A 1 HETATM 6 C C6 NAG . . . K 2 1.04 -5.567 41.4 1 96.04 ? C6 NAG 502 A 1 HETATM 7 C C7 NAG . . . K 2 -5.363 -4.494 40.308 1 97.9 ? C7 NAG 502 A 1 HETATM 8 C C8 NAG . . . K 2 -6.481 -3.983 39.444 1 88.72 ? C8 NAG 502 A 1 HETATM 9 N N2 NAG . . . K 2 -4.198 -3.852 40.189 1 97.97 ? N2 NAG 502 A 1 HETATM 10 O O3 NAG . . . K 2 -2.281 -1.918 41.239 1 103.38 ? O3 NAG 502 A 1 HETATM 11 O O4 NAG . . . K 2 0.475 -2.737 40.879 1 110.64 ? O4 NAG 502 A 1 HETATM 12 O O5 NAG . . . K 2 -1.296 -5.9 41.217 1 113.57 ? O5 NAG 502 A 1 HETATM 13 O O6 NAG . . . K 2 1.51 -6.682 40.655 1 107.1 ? O6 NAG 502 A 1 HETATM 14 O O7 NAG . . . K 2 -5.52 -5.438 41.076 1 98.56 ? O7 NAG 502 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #