data_2V5Y # _model_server_result.job_id VAr1irfzpukXWcVrC3x-1g _model_server_result.datetime_utc '2024-11-22 13:32:43' _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 2v5y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1572}' # _entry.id 2V5Y # _exptl.entry_id 2V5Y _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 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.52 _cell.angle_gamma 90 _cell.entry_id 2V5Y _cell.length_a 167.336 _cell.length_b 69.325 _cell.length_c 97.487 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2V5Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_755 -x+2,y,-z -1 0 0 0 1 0 0 0 -1 334.672 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 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 7 A CYS 7 1_555 A SG CYS 16 A CYS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 76 A CYS 76 1_555 A SG CYS 162 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 186 A CYS 186 1_555 A SG CYS 240 A CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 356 A CYS 356 1_555 A SG CYS 390 A CYS 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 52 A ASN 52 1_555 E C1 NAG . A NAG 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 72 A ASN 72 1_555 C C1 NAG . A NAG 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 111 A ASN 111 1_555 D C1 NAG . A NAG 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 A ND2 ASN 386 A ASN 386 1_555 B C1 NAG . A NAG 1569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 A ND2 ASN 394 A ASN 394 1_555 G C1 NAG . A NAG 1574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 A ND2 ASN 434 A ASN 434 1_555 F C1 NAG . A NAG 1573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 A ND2 ASN 524 A ASN 524 1_555 H C1 NAG . A NAG 1575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? metalc ? metalc1 A OD1 ASP 24 A ASP 24 1_555 I NA NA . A NA 1576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc2 A OD1 ASN 27 A ASN 27 1_555 I NA NA . A NA 1576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc3 A OD1 ASP 153 A ASP 153 1_555 J NA NA . A NA 1577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? # _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 2V5Y _atom_sites.fract_transf_matrix[1][1] 0.005976 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002601 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014425 _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] 0.011187 _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 B 2 NAG A 1 1569 1569 NAG NAG . C 2 NAG A 1 1570 1570 NAG NAG . D 2 NAG A 1 1571 1571 NAG NAG . E 2 NAG A 1 1572 1572 NAG NAG . F 2 NAG A 1 1573 1573 NAG NAG . G 2 NAG A 1 1574 1574 NAG NAG . H 2 NAG A 1 1575 1575 NAG NAG . I 3 NA A 1 1576 1576 NA NA . J 3 NA A 1 1577 1577 NA NA . # 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 . . . E 2 227.16 68.137 22.873 1 51.54 ? C1 NAG 1572 A 1 HETATM 2 C C2 NAG . . . E 2 228.445 68.166 22.044 1 52.17 ? C2 NAG 1572 A 1 HETATM 3 C C3 NAG . . . E 2 229.583 67.543 22.838 1 52.35 ? C3 NAG 1572 A 1 HETATM 4 C C4 NAG . . . E 2 229.733 68.315 24.136 1 52.35 ? C4 NAG 1572 A 1 HETATM 5 C C5 NAG . . . E 2 228.409 68.301 24.902 1 52.47 ? C5 NAG 1572 A 1 HETATM 6 C C6 NAG . . . E 2 228.505 69.151 26.173 1 52.73 ? C6 NAG 1572 A 1 HETATM 7 C C7 NAG . . . E 2 228.534 68.031 19.605 1 53.01 ? C7 NAG 1572 A 1 HETATM 8 C C8 NAG . . . E 2 228.089 69.464 19.431 1 52.97 ? C8 NAG 1572 A 1 HETATM 9 N N2 NAG . . . E 2 228.311 67.456 20.791 1 52.62 ? N2 NAG 1572 A 1 HETATM 10 O O3 NAG . . . E 2 230.779 67.594 22.091 1 52.4 ? O3 NAG 1572 A 1 HETATM 11 O O4 NAG . . . E 2 230.742 67.687 24.884 1 52.38 ? O4 NAG 1572 A 1 HETATM 12 O O5 NAG . . . E 2 227.383 68.845 24.085 1 52 ? O5 NAG 1572 A 1 HETATM 13 O O6 NAG . . . E 2 227.715 68.604 27.212 1 53.11 ? O6 NAG 1572 A 1 HETATM 14 O O7 NAG . . . E 2 229.07 67.416 18.676 1 52.98 ? O7 NAG 1572 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #