data_6WY5 # _model_server_result.job_id DQFGkGeljGeIItXYp4tlcQ _model_server_result.datetime_utc '2024-11-18 21:36:20' _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 6wy5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":601}' # _entry.id 6WY5 # _exptl.entry_id 6WY5 _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 1 _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 6WY5 _cell.length_a 107.902 _cell.length_b 107.902 _cell.length_c 240.141 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J,K,L,M 1 1 C,D,G,H,N,O,P,Q,R 2 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 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id P _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 4 5 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 4 6 1 FUC NAG C1 O1 . O6 HO6 . 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 3 n E NAG 1 C 1 NAG B 630 NAG 3 n E NAG 2 C 2 NAG B 631 NAG 4 n F NAG 1 F 1 NAG B 640 NAG 4 n F NAG 2 F 2 NAG B 641 NAG 4 n F BMA 3 F 3 BMA B 642 BMA 4 n F MAN 4 F 4 MAN B 643 MAN 4 n F MAN 5 F 5 MAN B 644 MAN 4 n F FUC 6 F 6 FUC B 645 FUC 3 n G NAG 1 G 1 NAG E 630 NAG 3 n G NAG 2 G 2 NAG E 631 NAG 4 n H NAG 1 H 1 NAG E 640 NAG 4 n H NAG 2 H 2 NAG E 641 NAG 4 n H BMA 3 H 3 BMA E 642 BMA 4 n H MAN 4 H 4 MAN E 643 MAN 4 n H MAN 5 H 5 MAN E 644 MAN 4 n H FUC 6 H 6 FUC E 645 FUC # 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 B SG CYS 3 B CYS 115 1_555 B SG CYS 13 B CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? disulf ? disulf2 B SG CYS 7 B CYS 119 1_555 B SG CYS 31 B CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? disulf ? disulf3 B SG CYS 41 B CYS 153 1_555 D SG CYS 41 E CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? disulf ? disulf4 D SG CYS 3 E CYS 115 1_555 D SG CYS 13 E CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? covale ? covale1 A OD1 ASP 94 A ASP 94 1_555 I CMD HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale2 I CMB HEC . A HEC 201 1_555 B OE2 GLU 130 B GLU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 I CBB HEC . A HEC 201 1_555 B SD MET 131 B MET 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.745 ? covale ? covale4 B C SER 37 B SER 149 1_555 B N CSO 38 B CSO 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale5 B C CSO 38 B CSO 150 1_555 B N PRO 39 B PRO 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale6 B ND2 ASN 113 B ASN 225 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale7 B ND2 ASN 205 B ASN 317 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale8 C OD1 ASP 94 D ASP 94 1_555 N CMD HEC . D HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale9 N CMB HEC . D HEC 201 1_555 D OE2 GLU 130 E GLU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale10 N CBB HEC . D HEC 201 1_555 D SD MET 131 E MET 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? covale ? covale11 D C SER 37 E SER 149 1_555 D N CSO 38 E CSO 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale12 D C CSO 38 E CSO 150 1_555 D N PRO 39 E PRO 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale13 D ND2 ASN 77 E ASN 189 1_555 P C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale14 D ND2 ASN 113 E ASN 225 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale15 D ND2 ASN 205 E ASN 317 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale16 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale18 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale19 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale20 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale21 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale22 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale23 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale24 H O6 NAG . H NAG 1 1_555 H C1 FUC . H FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale25 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale26 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale27 H O6 BMA . H BMA 3 1_555 H C1 MAN . H MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? metalc ? metalc1 A O ASP 96 A ASP 96 1_555 K CA CA . B CA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc2 A OD1 ASP 96 A ASP 96 1_555 K CA CA . B CA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc3 I FE HEC . A HEC 201 1_555 B NE2 HIS 224 B HIS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc4 B O THR 56 B THR 168 1_555 K CA CA . B CA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc5 B OG1 THR 56 B THR 168 1_555 K CA CA . B CA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc6 B O PHE 58 B PHE 170 1_555 K CA CA . B CA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc7 B OD1 ASP 60 B ASP 172 1_555 K CA CA . B CA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc8 B OG SER 62 B SER 174 1_555 K CA CA . B CA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc9 C O ASP 96 D ASP 96 1_555 Q CA CA . E CA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc10 C OD1 ASP 96 D ASP 96 1_555 Q CA CA . E CA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc11 N FE HEC . D HEC 201 1_555 D NE2 HIS 224 E HIS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc12 D O THR 56 E THR 168 1_555 Q CA CA . E CA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc13 D OG1 THR 56 E THR 168 1_555 Q CA CA . E CA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc14 D O PHE 58 E PHE 170 1_555 Q CA CA . E CA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc15 D OD1 ASP 60 E ASP 172 1_555 Q CA CA . E CA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc16 D OG SER 62 E SER 174 1_555 Q CA CA . E CA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? # _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 404 n n C1 O1 NAG sing 405 n n C1 O5 NAG sing 406 n n C1 H1 NAG sing 407 n n C2 C3 NAG sing 408 n n C2 N2 NAG sing 409 n n C2 H2 NAG sing 410 n n C3 C4 NAG sing 411 n n C3 O3 NAG sing 412 n n C3 H3 NAG sing 413 n n C4 C5 NAG sing 414 n n C4 O4 NAG sing 415 n n C4 H4 NAG sing 416 n n C5 C6 NAG sing 417 n n C5 O5 NAG sing 418 n n C5 H5 NAG sing 419 n n C6 O6 NAG sing 420 n n C6 H61 NAG sing 421 n n C6 H62 NAG sing 422 n n C7 C8 NAG sing 423 n n C7 N2 NAG sing 424 n n C7 O7 NAG doub 425 n n C8 H81 NAG sing 426 n n C8 H82 NAG sing 427 n n C8 H83 NAG sing 428 n n N2 HN2 NAG sing 429 n n O1 HO1 NAG sing 430 n n O3 HO3 NAG sing 431 n n O4 HO4 NAG sing 432 n n O6 HO6 NAG sing 433 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 6WY5 _atom_sites.fract_transf_matrix[1][1] 0.009268 _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] 0.009268 _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] 0.004164 _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 5 HEC A 1 201 605 HEC HEM . J 6 CL A 1 202 1 CL CL . K 7 CA B 1 609 1 CA CA . L 6 CL B 1 610 2 CL CL . M 8 UF7 B 1 611 1 UF7 LG1 . N 5 HEC D 1 201 605 HEC HEM . O 6 CL D 1 202 3 CL CL . P 9 NAG E 1 601 620 NAG NAG . Q 7 CA E 1 610 2 CA CA . R 8 UF7 E 1 611 2 UF7 LG1 . # 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 . . . P 9 23.472 -69.897 26.601 1 101.29 ? C1 NAG 601 E 1 HETATM 2 C C2 NAG . . . P 9 23.532 -70.342 28.061 1 101.1 ? C2 NAG 601 E 1 HETATM 3 C C3 NAG . . . P 9 24.124 -71.749 28.095 1 102.08 ? C3 NAG 601 E 1 HETATM 4 C C4 NAG . . . P 9 23.274 -72.716 27.274 1 102.76 ? C4 NAG 601 E 1 HETATM 5 C C5 NAG . . . P 9 23.025 -72.19 25.859 1 102.35 ? C5 NAG 601 E 1 HETATM 6 C C6 NAG . . . P 9 21.932 -72.966 25.146 1 102.25 ? C6 NAG 601 E 1 HETATM 7 C C7 NAG . . . P 9 23.779 -68.373 29.5 1 99.16 ? C7 NAG 601 E 1 HETATM 8 C C8 NAG . . . P 9 24.729 -67.539 30.306 1 98.84 ? C8 NAG 601 E 1 HETATM 9 N N2 NAG . . . P 9 24.309 -69.437 28.893 1 100.13 ? N2 NAG 601 E 1 HETATM 10 O O3 NAG . . . P 9 24.157 -72.187 29.448 1 102.44 ? O3 NAG 601 E 1 HETATM 11 O O4 NAG . . . P 9 23.89 -74.011 27.226 1 103.66 ? O4 NAG 601 E 1 HETATM 12 O O5 NAG . . . P 9 22.607 -70.806 25.906 1 101.82 ? O5 NAG 601 E 1 HETATM 13 O O6 NAG . . . P 9 21.432 -72.307 23.986 1 102.24 ? O6 NAG 601 E 1 HETATM 14 O O7 NAG . . . P 9 22.589 -68.087 29.39 1 98.76 ? O7 NAG 601 E 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #