data_3W12 # _model_server_result.job_id Xcme7I_33Qd47HsjAo4v5A _model_server_result.datetime_utc '2024-11-05 00:36:18' _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 3w12 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":406}' # _entry.id 3W12 # _exptl.entry_id 3W12 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 9 _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 3W12 _cell.length_a 169.488 _cell.length_b 169.488 _cell.length_c 169.488 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3W12 _symmetry.cell_setting ? _symmetry.Int_Tables_number 195 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 # _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 ? 9 I N N ? 9 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 7 oligosaccharide 8 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 7 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 7 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 8 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 8 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 7 n G NAG 1 G 1 NAG E 531 NAG 7 n G NAG 2 G 2 NAG E 532 NAG 7 n G BMA 3 G 3 BMA E 533 BMA 7 n G MAN 4 G 4 MAN E 534 MAN 8 n H NAG 1 H 1 NAG E 551 NAG 8 n H NAG 2 H 2 NAG E 553 NAG 8 n H BMA 3 H 3 BMA E 554 BMA # 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 8 E CYS 8 1_555 A SG CYS 26 E CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 126 E CYS 126 1_555 A SG CYS 155 E CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf3 A SG CYS 159 E CYS 159 1_555 A SG CYS 182 E CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf4 A SG CYS 169 E CYS 169 1_555 A SG CYS 188 E CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 A SG CYS 192 E CYS 192 1_555 A SG CYS 201 E CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 A SG CYS 196 E CYS 196 1_555 A SG CYS 207 E CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 A SG CYS 208 E CYS 208 1_555 A SG CYS 216 E CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 A SG CYS 212 E CYS 212 1_555 A SG CYS 225 E CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 A SG CYS 228 E CYS 228 1_555 A SG CYS 237 E CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf10 A SG CYS 241 E CYS 241 1_555 A SG CYS 253 E CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf11 A SG CYS 259 E CYS 259 1_555 A SG CYS 284 E CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 A SG CYS 288 E CYS 288 1_555 A SG CYS 301 E CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf13 A SG CYS 304 E CYS 304 1_555 A SG CYS 308 E CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf14 B SG CYS 22 C CYS 22 1_555 B SG CYS 95 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf15 C SG CYS 23 D CYS 23 1_555 C SG CYS 94 D CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? disulf ? disulf16 D SG CYS 6 A CYS 6 1_555 D SG CYS 11 A CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf17 D SG CYS 7 A CYS 7 1_555 E SG CYS 7 B CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf18 D SG CYS 20 A CYS 20 1_555 E SG CYS 19 B CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? covale ? covale1 A ND2 ASN 25 E ASN 25 1_555 I C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 A ND2 ASN 111 E ASN 111 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 A ND2 ASN 215 E ASN 215 1_555 J C1 NAG . E NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 A ND2 ASN 255 E ASN 255 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale5 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale7 G O3 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 3W12 _atom_sites.fract_transf_matrix[1][1] 0.0059 _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] 0.0059 _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] 0.0059 _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 I 9 NAG E 1 401 511 NAG NAG . J 9 NAG E 1 406 541 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 . . . J 9 39.786 13.479 79.35 1 227.77 ? C1 NAG 406 E 1 HETATM 2 C C2 NAG . . . J 9 40.77 13.559 78.188 1 240.51 ? C2 NAG 406 E 1 HETATM 3 C C3 NAG . . . J 9 42.136 12.962 78.565 1 252.84 ? C3 NAG 406 E 1 HETATM 4 C C4 NAG . . . J 9 42.671 13.533 79.872 1 251.92 ? C4 NAG 406 E 1 HETATM 5 C C5 NAG . . . J 9 41.564 13.612 80.934 1 252.87 ? C5 NAG 406 E 1 HETATM 6 C C6 NAG . . . J 9 42.068 14.364 82.164 1 262.38 ? C6 NAG 406 E 1 HETATM 7 C C7 NAG . . . J 9 39.905 11.669 76.809 1 231.52 ? C7 NAG 406 E 1 HETATM 8 C C8 NAG . . . J 9 39.343 11.343 75.462 1 237.36 ? C8 NAG 406 E 1 HETATM 9 N N2 NAG . . . J 9 40.208 12.953 76.99 1 233.08 ? N2 NAG 406 E 1 HETATM 10 O O3 NAG . . . J 9 43.09 13.233 77.563 1 274.65 ? O3 NAG 406 E 1 HETATM 11 O O4 NAG . . . J 9 43.768 12.747 80.309 1 241.21 ? O4 NAG 406 E 1 HETATM 12 O O5 NAG . . . J 9 40.354 14.197 80.435 1 236.32 ? O5 NAG 406 E 1 HETATM 13 O O6 NAG . . . J 9 42.341 15.706 81.83 1 262.67 ? O6 NAG 406 E 1 HETATM 14 O O7 NAG . . . J 9 40.053 10.78 77.648 1 234.62 ? O7 NAG 406 E 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #