data_5VRP # _model_server_result.job_id S8F7AxAJXi4zwheFN7ByTw _model_server_result.datetime_utc '2024-11-16 23:56:03' _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 5vrp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 5VRP # _exptl.entry_id 5VRP _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 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 90 _cell.entry_id 5VRP _cell.length_a 54.334 _cell.length_b 99.933 _cell.length_c 146.529 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VRP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F 1 1 B,G,H,I,J 2 1 A,B,C,D,E,F,G,H,I,J 3 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 G 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 48 A CYS 117 1_555 A SG CYS 55 A CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 214 A CYS 283 1_555 A SG CYS 218 A CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 256 A CYS 325 1_555 A SG CYS 293 A CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 48 B CYS 117 1_555 B SG CYS 55 B CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 214 B CYS 283 1_555 B SG CYS 218 B CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 256 B CYS 325 1_555 B SG CYS 293 B CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 B ND2 ASN 72 B ASN 141 1_555 G C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 317 n n C1 O1 NAG sing 318 n n C1 O5 NAG sing 319 n n C1 H1 NAG sing 320 n n C2 C3 NAG sing 321 n n C2 N2 NAG sing 322 n n C2 H2 NAG sing 323 n n C3 C4 NAG sing 324 n n C3 O3 NAG sing 325 n n C3 H3 NAG sing 326 n n C4 C5 NAG sing 327 n n C4 O4 NAG sing 328 n n C4 H4 NAG sing 329 n n C5 C6 NAG sing 330 n n C5 O5 NAG sing 331 n n C5 H5 NAG sing 332 n n C6 O6 NAG sing 333 n n C6 H61 NAG sing 334 n n C6 H62 NAG sing 335 n n C7 C8 NAG sing 336 n n C7 N2 NAG sing 337 n n C7 O7 NAG doub 338 n n C8 H81 NAG sing 339 n n C8 H82 NAG sing 340 n n C8 H83 NAG sing 341 n n N2 HN2 NAG sing 342 n n O1 HO1 NAG sing 343 n n O3 HO3 NAG sing 344 n n O4 HO4 NAG sing 345 n n O6 HO6 NAG sing 346 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 5VRP _atom_sites.fract_transf_matrix[1][1] 0.018405 _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] 0.010007 _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] 0.006825 _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 A 1 501 459 NAG NAG . D 3 SO4 A 1 502 2 SO4 SO4 . E 4 9JD A 1 503 1 9JD 604 . F 4 9JD A 1 504 4 9JD 604 . G 2 NAG B 1 501 459 NAG NAG . H 4 9JD B 1 502 2 9JD 604 . I 4 9JD B 1 503 3 9JD 604 . J 5 HOH B 1 601 2 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 . . . G 2 10.207 32.321 51.784 1 71.07 ? C1 NAG 501 B 1 HETATM 2 C C2 NAG . . . G 2 10.261 32.792 53.23 1 71.77 ? C2 NAG 501 B 1 HETATM 3 C C3 NAG . . . G 2 11.171 31.892 54.032 1 72.19 ? C3 NAG 501 B 1 HETATM 4 C C4 NAG . . . G 2 10.489 30.548 54.198 1 73.25 ? C4 NAG 501 B 1 HETATM 5 C C5 NAG . . . G 2 10.085 29.947 52.85 1 72.85 ? C5 NAG 501 B 1 HETATM 6 C C6 NAG . . . G 2 8.639 29.509 52.814 1 72.66 ? C6 NAG 501 B 1 HETATM 7 C C7 NAG . . . G 2 9.901 35.221 53.371 1 71.27 ? C7 NAG 501 B 1 HETATM 8 C C8 NAG . . . G 2 10.563 36.565 53.444 1 71.18 ? C8 NAG 501 B 1 HETATM 9 N N2 NAG . . . G 2 10.723 34.169 53.305 1 71.7 ? N2 NAG 501 B 1 HETATM 10 O O3 NAG . . . G 2 11.413 32.474 55.308 1 71.49 ? O3 NAG 501 B 1 HETATM 11 O O4 NAG . . . G 2 11.372 29.648 54.857 1 74.93 ? O4 NAG 501 B 1 HETATM 12 O O5 NAG . . . G 2 10.246 30.834 51.721 1 71.89 ? O5 NAG 501 B 1 HETATM 13 O O6 NAG . . . G 2 8.51 28.1 52.936 1 72.6 ? O6 NAG 501 B 1 HETATM 14 O O7 NAG . . . G 2 8.681 35.096 53.371 1 71.5 ? O7 NAG 501 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #