data_3D66 # _model_server_result.job_id VVDOFuKJ90qLADTPnHbHeg _model_server_result.datetime_utc '2024-11-06 05:57:05' _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 3d66 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 3D66 # _exptl.entry_id 3D66 _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 9 _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 3D66 _cell.length_a 161.74 _cell.length_b 161.74 _cell.length_c 139.45 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D66 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_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,D,E,F,G,H 1 1 B,I,J,K,L,M 2 1 C,N,O 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 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 N 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 179 A CYS 156 1_555 A SG CYS 192 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 251 A CYS 228 1_555 A SG CYS 275 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf3 A SG CYS 266 A CYS 243 1_555 A SG CYS 280 A CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? disulf ? disulf4 B SG CYS 179 B CYS 156 1_555 B SG CYS 192 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf5 B SG CYS 251 B CYS 228 1_555 B SG CYS 275 B CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf6 B SG CYS 266 B CYS 243 1_555 B SG CYS 280 B CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf7 C SG CYS 179 C CYS 156 1_555 C SG CYS 192 C CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf8 C SG CYS 251 C CYS 228 1_555 C SG CYS 275 C CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf9 C SG CYS 266 C CYS 243 1_555 C SG CYS 280 C CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? covale ? covale1 A ND2 ASN 45 A ASN 22 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 74 A ASN 51 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 A ND2 ASN 86 A ASN 63 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale4 A ND2 ASN 109 A ASN 86 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale5 B ND2 ASN 45 B ASN 22 1_555 I C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale6 B ND2 ASN 74 B ASN 51 1_555 J C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale7 B ND2 ASN 86 B ASN 63 1_555 K C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale8 B ND2 ASN 109 B ASN 86 1_555 L C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale9 C ND2 ASN 109 C ASN 86 1_555 N C1 NAG . C NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? metalc ? metalc1 A ND1 HIS 182 A HIS 159 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc2 A OE1 GLU 185 A GLU 162 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc3 A OE2 GLU 185 A GLU 162 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc4 A ND1 HIS 311 A HIS 288 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc5 B ND1 HIS 182 B HIS 159 1_555 M ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc6 B OE1 GLU 185 B GLU 162 1_555 M ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc7 B OE2 GLU 185 B GLU 162 1_555 M ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc8 B ND1 HIS 311 B HIS 288 1_555 M ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc9 C ND1 HIS 182 C HIS 159 1_555 O ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 C OE1 GLU 185 C GLU 162 1_555 O ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc11 C OE2 GLU 185 C GLU 162 1_555 O ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc12 C ND1 HIS 311 C HIS 288 1_555 O ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? # _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 3D66 _atom_sites.fract_transf_matrix[1][1] 0.006183 _atom_sites.fract_transf_matrix[1][2] 0.00357 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007139 _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] 0.007171 _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 2 NAG A 1 601 601 NAG NAG . E 2 NAG A 1 602 602 NAG NAG . F 2 NAG A 1 603 603 NAG NAG . G 2 NAG A 1 604 604 NAG NAG . H 3 ZN A 1 501 501 ZN ZN . I 2 NAG B 1 601 601 NAG NAG . J 2 NAG B 1 602 602 NAG NAG . K 2 NAG B 1 603 603 NAG NAG . L 2 NAG B 1 604 604 NAG NAG . M 3 ZN B 1 501 501 ZN ZN . N 2 NAG C 1 604 604 NAG NAG . O 3 ZN C 1 501 501 ZN ZN . # 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 . . . D 2 57.192 50.842 62.774 1 104.01 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . D 2 58.397 51.688 63.247 1 105.24 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . D 2 59.237 51.091 64.418 1 106.91 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . D 2 58.522 50.051 65.313 1 107.68 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . D 2 57.531 49.22 64.464 1 107.81 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . D 2 56.674 48.205 65.225 1 108.9 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . D 2 59.565 52.999 61.508 1 101.98 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . D 2 60.202 54.078 62.351 1 101.67 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . D 2 59.272 51.849 62.091 1 103.05 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . D 2 59.835 52.115 65.21 1 107 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . D 2 59.499 49.264 66.011 1 107.81 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . D 2 56.625 50.103 63.833 1 105.88 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . D 2 55.645 47.727 64.365 1 109.97 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . D 2 59.345 53.155 60.311 1 101.34 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #