data_6VY5 # _model_server_result.job_id lljaINa41HBaFJj9VXLExQ _model_server_result.datetime_utc '2024-10-19 12:24:17' _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 6vy5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":705}' # _entry.id 6VY5 # _exptl.entry_id 6VY5 _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 5 _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 6VY5 _cell.length_a 186.701 _cell.length_b 186.701 _cell.length_c 81.312 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _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 ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H 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 22 H CYS 22 1_555 A SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 154 H CYS 154 1_555 A SG CYS 210 H CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 22 L CYS 23 1_555 B SG CYS 87 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 136 L CYS 137 1_555 B SG CYS 195 L CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 C SG CYS 7 A CYS 189 1_555 C SG CYS 419 A CYS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 C SG CYS 100 A CYS 282 1_555 C SG CYS 113 A CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 C SG CYS 200 A CYS 382 1_555 C SG CYS 213 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 C SG CYS 205 A CYS 387 1_555 C SG CYS 317 A CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 C SG CYS 311 A CYS 493 1_555 C SG CYS 321 A CYS 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 C SG CYS 383 A CYS 565 1_555 C SG CYS 392 A CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 C ND2 ASN 124 A ASN 306 1_555 E C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 C ND2 ASN 196 A ASN 378 1_555 D C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 C ND2 ASN 235 A ASN 417 1_555 F C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 C ND2 ASN 299 A ASN 481 1_555 G C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 C ND2 ASN 347 A ASN 529 1_555 H C1 NAG . A NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 6VY5 _atom_sites.fract_transf_matrix[1][1] 0.005356 _atom_sites.fract_transf_matrix[1][2] 0.003092 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006185 _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] 0.012298 _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 1 701 603 NAG NAG . E 4 NAG A 1 702 604 NAG NAG . F 4 NAG A 1 703 605 NAG NAG . G 4 NAG A 1 704 606 NAG NAG . H 4 NAG A 1 705 607 NAG NAG . # 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 . . . H 4 61.148 -59.275 -4.816 1 62.06 ? C1 NAG 705 A 1 HETATM 2 C C2 NAG . . . H 4 60.684 -57.982 -4.144 1 59.28 ? C2 NAG 705 A 1 HETATM 3 C C3 NAG . . . H 4 60.357 -58.235 -2.675 1 59.96 ? C3 NAG 705 A 1 HETATM 4 C C4 NAG . . . H 4 59.362 -59.38 -2.543 1 51.77 ? C4 NAG 705 A 1 HETATM 5 C C5 NAG . . . H 4 59.885 -60.615 -3.268 1 48.45 ? C5 NAG 705 A 1 HETATM 6 C C6 NAG . . . H 4 58.899 -61.76 -3.274 1 59.97 ? C6 NAG 705 A 1 HETATM 7 C C7 NAG . . . H 4 61.387 -55.635 -4.312 1 67.1 ? C7 NAG 705 A 1 HETATM 8 C C8 NAG . . . H 4 62.547 -54.697 -4.449 1 72.79 ? C8 NAG 705 A 1 HETATM 9 N N2 NAG . . . H 4 61.688 -56.938 -4.272 1 61.61 ? N2 NAG 705 A 1 HETATM 10 O O3 NAG . . . H 4 59.818 -57.053 -2.096 1 74.19 ? O3 NAG 705 A 1 HETATM 11 O O4 NAG . . . H 4 59.156 -59.693 -1.17 1 63.76 ? O4 NAG 705 A 1 HETATM 12 O O5 NAG . . . H 4 60.153 -60.294 -4.641 1 52.38 ? O5 NAG 705 A 1 HETATM 13 O O6 NAG . . . H 4 58.624 -62.2 -4.596 1 68.07 ? O6 NAG 705 A 1 HETATM 14 O O7 NAG . . . H 4 60.23 -55.233 -4.241 1 65.64 ? O7 NAG 705 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #