data_8YSH # _model_server_result.job_id amHIi37SufkvqPCPyFwJ2Q _model_server_result.datetime_utc '2024-11-27 16:48:30' _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 8ysh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 8YSH # _exptl.entry_id 8YSH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _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 8YSH _cell.length_a 58.488 _cell.length_b 58.488 _cell.length_c 351.625 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YSH _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 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 3 n C NAG 1 C 1 NAG B 591 NAG 3 n C NAG 2 C 2 NAG B 592 NAG 3 n C BMA 3 C 3 BMA B 593 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 3 B CYS 383 1_555 A SG CYS 27 B CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 45 B CYS 425 1_555 A SG CYS 98 B CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 A SG CYS 57 B CYS 437 1_555 A SG CYS 205 B CYS 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf4 A SG CYS 123 B CYS 503 1_555 A SG CYS 146 B CYS 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf5 B SG CYS 22 A CYS 22 1_555 B SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 A ND2 ASN 30 B ASN 410 1_555 D C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A ND2 ASN 107 B ASN 487 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 8YSH _atom_sites.fract_transf_matrix[1][1] 0.017098 _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] 0.017098 _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] 0.002844 _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 4 NAG B 1 601 590 NAG NAG . E 5 HOH B 1 701 8 HOH HOH . E 5 HOH B 2 702 22 HOH HOH . E 5 HOH B 3 703 23 HOH HOH . E 5 HOH B 4 704 29 HOH HOH . E 5 HOH B 5 705 49 HOH HOH . E 5 HOH B 6 706 87 HOH HOH . E 5 HOH B 7 707 25 HOH HOH . E 5 HOH B 8 708 5 HOH HOH . E 5 HOH B 9 709 15 HOH HOH . E 5 HOH B 10 710 6 HOH HOH . E 5 HOH B 11 711 12 HOH HOH . E 5 HOH B 12 712 56 HOH HOH . E 5 HOH B 13 713 61 HOH HOH . E 5 HOH B 14 714 39 HOH HOH . E 5 HOH B 15 715 18 HOH HOH . E 5 HOH B 16 716 68 HOH HOH . E 5 HOH B 17 717 2 HOH HOH . E 5 HOH B 18 718 37 HOH HOH . E 5 HOH B 19 719 14 HOH HOH . E 5 HOH B 20 720 31 HOH HOH . E 5 HOH B 21 721 30 HOH HOH . E 5 HOH B 22 722 38 HOH HOH . E 5 HOH B 23 723 63 HOH HOH . E 5 HOH B 24 724 1 HOH HOH . E 5 HOH B 25 725 79 HOH HOH . E 5 HOH B 26 726 19 HOH HOH . E 5 HOH B 27 727 60 HOH HOH . E 5 HOH B 28 728 69 HOH HOH . E 5 HOH B 29 729 48 HOH HOH . E 5 HOH B 30 730 78 HOH HOH . E 5 HOH B 31 731 24 HOH HOH . E 5 HOH B 32 732 52 HOH HOH . E 5 HOH B 33 733 50 HOH HOH . E 5 HOH B 34 734 40 HOH HOH . E 5 HOH B 35 735 86 HOH HOH . E 5 HOH B 36 736 83 HOH HOH . F 5 HOH A 1 201 35 HOH HOH . F 5 HOH A 2 202 55 HOH HOH . F 5 HOH A 3 203 26 HOH HOH . F 5 HOH A 4 204 28 HOH HOH . F 5 HOH A 5 205 4 HOH HOH . F 5 HOH A 6 206 36 HOH HOH . F 5 HOH A 7 207 9 HOH HOH . F 5 HOH A 8 208 58 HOH HOH . F 5 HOH A 9 209 13 HOH HOH . F 5 HOH A 10 210 21 HOH HOH . F 5 HOH A 11 211 45 HOH HOH . F 5 HOH A 12 212 54 HOH HOH . F 5 HOH A 13 213 74 HOH HOH . F 5 HOH A 14 214 43 HOH HOH . F 5 HOH A 15 215 16 HOH HOH . F 5 HOH A 16 216 10 HOH HOH . F 5 HOH A 17 217 11 HOH HOH . F 5 HOH A 18 218 7 HOH HOH . F 5 HOH A 19 219 17 HOH HOH . F 5 HOH A 20 220 70 HOH HOH . F 5 HOH A 21 221 57 HOH HOH . F 5 HOH A 22 222 72 HOH HOH . F 5 HOH A 23 223 73 HOH HOH . F 5 HOH A 24 224 41 HOH HOH . F 5 HOH A 25 225 33 HOH HOH . F 5 HOH A 26 226 71 HOH HOH . F 5 HOH A 27 227 65 HOH HOH . F 5 HOH A 28 228 27 HOH HOH . F 5 HOH A 29 229 66 HOH HOH . F 5 HOH A 30 230 59 HOH HOH . F 5 HOH A 31 231 20 HOH HOH . F 5 HOH A 32 232 84 HOH HOH . F 5 HOH A 33 233 64 HOH HOH . F 5 HOH A 34 234 53 HOH HOH . F 5 HOH A 35 235 42 HOH HOH . F 5 HOH A 36 236 46 HOH HOH . F 5 HOH A 37 237 51 HOH HOH . F 5 HOH A 38 238 85 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 . . . D 4 36.215 31.818 -14.678 1 101.16 ? C1 NAG 601 B 1 HETATM 2 C C2 NAG . . . D 4 37.419 32.725 -14.466 1 107.75 ? C2 NAG 601 B 1 HETATM 3 C C3 NAG . . . D 4 37.109 34.132 -14.941 1 111.93 ? C3 NAG 601 B 1 HETATM 4 C C4 NAG . . . D 4 36.661 34.092 -16.389 1 113.04 ? C4 NAG 601 B 1 HETATM 5 C C5 NAG . . . D 4 35.484 33.144 -16.54 1 105.66 ? C5 NAG 601 B 1 HETATM 6 C C6 NAG . . . D 4 35.098 32.993 -18.002 1 98.86 ? C6 NAG 601 B 1 HETATM 7 C C7 NAG . . . D 4 38.729 31.948 -12.596 1 104.28 ? C7 NAG 601 B 1 HETATM 8 C C8 NAG . . . D 4 38.625 31.613 -11.14 1 106.79 ? C8 NAG 601 B 1 HETATM 9 N N2 NAG . . . D 4 37.796 32.763 -13.07 1 105.71 ? N2 NAG 601 B 1 HETATM 10 O O3 NAG . . . D 4 38.281 34.943 -14.824 1 114.11 ? O3 NAG 601 B 1 HETATM 11 O O4 NAG . . . D 4 36.274 35.404 -16.802 1 115.64 ? O4 NAG 601 B 1 HETATM 12 O O5 NAG . . . D 4 35.824 31.855 -16.047 1 103.36 ? O5 NAG 601 B 1 HETATM 13 O O6 NAG . . . D 4 36.055 32.147 -18.646 1 94.94 ? O6 NAG 601 B 1 HETATM 14 O O7 NAG . . . D 4 39.613 31.502 -13.303 1 104.05 ? O7 NAG 601 B 1 # _model_server_stats.io_time_ms 100 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #