data_6YA0 # _model_server_result.job_id ipn5sE5lJM3fhWsQ3Ai1Ng _model_server_result.datetime_utc '2024-11-09 02:34:02' _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 6ya0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":603}' # _entry.id 6YA0 # _exptl.entry_id 6YA0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 103.27 _cell.angle_gamma 90 _cell.entry_id 6YA0 _cell.length_a 68.82 _cell.length_b 74.85 _cell.length_c 81.28 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YA0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 dimeric 2 author_and_software_defined_assembly 1 PISA monomeric 1 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,G,H,I,L,M 1 1 C,D,J,K,N 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 H N N ? 3 I N N ? 3 J N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 BMA _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 2 n D NAG 1 D 1 NAG C 450 NAG 2 n D BMA 2 D 2 BMA C 451 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 79 A CYS 114 1_555 A SG CYS 110 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 87 A CYS 122 1_555 A SG CYS 121 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf3 A SG CYS 189 A CYS 224 1_555 A SG CYS 250 A CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 B SG CYS 79 B CYS 114 1_555 B SG CYS 110 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf5 B SG CYS 87 B CYS 122 1_555 B SG CYS 121 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 189 B CYS 224 1_555 B SG CYS 250 B CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 C SG CYS 79 C CYS 114 1_555 C SG CYS 110 C CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf8 C SG CYS 87 C CYS 122 1_555 C SG CYS 121 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf9 C SG CYS 189 C CYS 224 1_555 C SG CYS 250 C CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 81 A ASN 116 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 175 A ASN 210 1_555 F C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 B ND2 ASN 81 B ASN 116 1_555 H C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 B ND2 ASN 175 B ASN 210 1_555 I C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 C ND2 ASN 81 C ASN 116 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 C ND2 ASN 175 C ASN 210 1_555 J C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 BMA . D BMA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _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 267 n n C1 O1 NAG sing 268 n n C1 O5 NAG sing 269 n n C1 H1 NAG sing 270 n n C2 C3 NAG sing 271 n n C2 N2 NAG sing 272 n n C2 H2 NAG sing 273 n n C3 C4 NAG sing 274 n n C3 O3 NAG sing 275 n n C3 H3 NAG sing 276 n n C4 C5 NAG sing 277 n n C4 O4 NAG sing 278 n n C4 H4 NAG sing 279 n n C5 C6 NAG sing 280 n n C5 O5 NAG sing 281 n n C5 H5 NAG sing 282 n n C6 O6 NAG sing 283 n n C6 H61 NAG sing 284 n n C6 H62 NAG sing 285 n n C7 C8 NAG sing 286 n n C7 N2 NAG sing 287 n n C7 O7 NAG doub 288 n n C8 H81 NAG sing 289 n n C8 H82 NAG sing 290 n n C8 H83 NAG sing 291 n n N2 HN2 NAG sing 292 n n O1 HO1 NAG sing 293 n n O3 HO3 NAG sing 294 n n O4 HO4 NAG sing 295 n n O6 HO6 NAG sing 296 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 6YA0 _atom_sites.fract_transf_matrix[1][1] 0.014531 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003427 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01336 _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] 0.012641 _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 E 3 NAG A 1 401 450 NAG NAG . F 3 NAG A 1 402 500 NAG NAG . G 4 ACT B 1 601 601 ACT ACT . H 3 NAG B 1 602 450 NAG NAG . I 3 NAG B 1 603 500 NAG NAG . J 3 NAG C 1 403 500 NAG NAG . K 5 NH4 C 1 404 1 NH4 NH4 . L 6 HOH A 1 501 37 HOH HOH . L 6 HOH A 2 502 12 HOH HOH . L 6 HOH A 3 503 36 HOH HOH . L 6 HOH A 4 504 27 HOH HOH . L 6 HOH A 5 505 7 HOH HOH . L 6 HOH A 6 506 18 HOH HOH . L 6 HOH A 7 507 33 HOH HOH . L 6 HOH A 8 508 34 HOH HOH . L 6 HOH A 9 509 35 HOH HOH . L 6 HOH A 10 510 32 HOH HOH . M 6 HOH B 1 701 25 HOH HOH . M 6 HOH B 2 702 2 HOH HOH . M 6 HOH B 3 703 19 HOH HOH . M 6 HOH B 4 704 26 HOH HOH . M 6 HOH B 5 705 24 HOH HOH . M 6 HOH B 6 706 15 HOH HOH . M 6 HOH B 7 707 11 HOH HOH . M 6 HOH B 8 708 28 HOH HOH . M 6 HOH B 9 709 20 HOH HOH . M 6 HOH B 10 710 38 HOH HOH . M 6 HOH B 11 711 14 HOH HOH . M 6 HOH B 12 712 31 HOH HOH . M 6 HOH B 13 713 4 HOH HOH . M 6 HOH B 14 714 29 HOH HOH . N 6 HOH C 1 501 5 HOH HOH . N 6 HOH C 2 502 16 HOH HOH . N 6 HOH C 3 503 23 HOH HOH . N 6 HOH C 4 504 3 HOH HOH . N 6 HOH C 5 505 13 HOH HOH . N 6 HOH C 6 506 30 HOH HOH . N 6 HOH C 7 507 1 HOH HOH . N 6 HOH C 8 508 9 HOH HOH . # 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 . . . I 3 -1.886 -26.584 -13.342 0 63.59 ? C1 NAG 603 B 1 HETATM 2 C C2 NAG . . . I 3 -2.378 -26.085 -14.707 0 57.45 ? C2 NAG 603 B 1 HETATM 3 C C3 NAG . . . I 3 -2.132 -27.137 -15.788 0 57.92 ? C3 NAG 603 B 1 HETATM 4 C C4 NAG . . . I 3 -0.676 -27.578 -15.786 0 58.07 ? C4 NAG 603 B 1 HETATM 5 C C5 NAG . . . I 3 -0.289 -28.058 -14.394 0 58.42 ? C5 NAG 603 B 1 HETATM 6 C C6 NAG . . . I 3 1.17 -28.429 -14.278 0 57.49 ? C6 NAG 603 B 1 HETATM 7 C C7 NAG . . . I 3 -4.366 -24.893 -15.512 0 52.1 ? C7 NAG 603 B 1 HETATM 8 C C8 NAG . . . I 3 -5.83 -24.645 -15.306 0 50.84 ? C8 NAG 603 B 1 HETATM 9 N N2 NAG . . . I 3 -3.788 -25.735 -14.65 0 54.34 ? N2 NAG 603 B 1 HETATM 10 O O3 NAG . . . I 3 -2.47 -26.593 -17.059 0 57.7 ? O3 NAG 603 B 1 HETATM 11 O O4 NAG . . . I 3 -0.479 -28.63 -16.724 0 60.33 ? O4 NAG 603 B 1 HETATM 12 O O5 NAG . . . I 3 -0.521 -27.009 -13.445 0 59.27 ? O5 NAG 603 B 1 HETATM 13 O O6 NAG . . . I 3 1.528 -28.691 -12.928 0 55.49 ? O6 NAG 603 B 1 HETATM 14 O O7 NAG . . . I 3 -3.736 -24.354 -16.416 0 51.66 ? O7 NAG 603 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #