data_8JR5 # _model_server_result.job_id Py7e3zLLR3wiyXJw6hJCeA _model_server_result.datetime_utc '2024-11-19 23:46:23' _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 8jr5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":701}' # _entry.id 8JR5 # _exptl.entry_id 8JR5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.69 _cell.angle_gamma 90 _cell.entry_id 8JR5 _cell.length_a 83.926 _cell.length_b 63.658 _cell.length_c 121.622 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JR5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G 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 NAG _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 C NAG 1 C 1 NAG B 607 NAG 2 n C NAG 2 C 2 NAG B 608 NAG # 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 2 A CYS 189 1_555 A SG CYS 414 A CYS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 29 A CYS 216 1_555 A SG CYS 53 A CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 95 A CYS 282 1_555 A SG CYS 108 A CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? disulf ? disulf4 A SG CYS 195 A CYS 382 1_555 A SG CYS 208 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf5 A SG CYS 200 A CYS 387 1_555 A SG CYS 312 A CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf6 A SG CYS 306 A CYS 493 1_555 A SG CYS 316 A CYS 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 A SG CYS 378 A CYS 565 1_555 A SG CYS 387 A CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf8 B SG CYS 2 B CYS 189 1_555 B SG CYS 414 B CYS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf9 B SG CYS 29 B CYS 216 1_555 B SG CYS 53 B CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 B SG CYS 95 B CYS 282 1_555 B SG CYS 108 B CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf11 B SG CYS 195 B CYS 382 1_555 B SG CYS 208 B CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 B SG CYS 200 B CYS 387 1_555 B SG CYS 312 B CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf13 B SG CYS 306 B CYS 493 1_555 B SG CYS 316 B CYS 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf14 B SG CYS 378 B CYS 565 1_555 B SG CYS 387 B CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? covale ? covale1 A ND2 ASN 230 A ASN 417 1_555 E C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale2 A ND2 ASN 342 A ASN 529 1_555 D C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale3 B ND2 ASN 119 B ASN 306 1_555 G C1 NAG . B NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale4 B ND2 ASN 230 B ASN 417 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale5 B ND2 ASN 342 B ASN 529 1_555 F C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? # _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 8JR5 _atom_sites.fract_transf_matrix[1][1] 0.011915 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001609 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015709 _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] 0.008297 _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 3 NAG A 1 701 604 NAG NAG . E 3 NAG A 1 702 605 NAG NAG . F 3 NAG B 1 701 604 NAG NAG . G 3 NAG B 1 702 606 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 . . . F 3 -16.758 -0.744 2.452 1 99.07 ? C1 NAG 701 B 1 HETATM 2 C C2 NAG . . . F 3 -17.188 0.706 2.518 1 95.22 ? C2 NAG 701 B 1 HETATM 3 C C3 NAG . . . F 3 -18.67 0.75 2.881 1 94.48 ? C3 NAG 701 B 1 HETATM 4 C C4 NAG . . . F 3 -19.482 0.015 1.81 1 97.33 ? C4 NAG 701 B 1 HETATM 5 C C5 NAG . . . F 3 -18.958 -1.412 1.558 1 95.99 ? C5 NAG 701 B 1 HETATM 6 C C6 NAG . . . F 3 -19.61 -2.087 0.354 1 97.06 ? C6 NAG 701 B 1 HETATM 7 C C7 NAG . . . F 3 -16.077 2.741 3.386 1 94.52 ? C7 NAG 701 B 1 HETATM 8 C C8 NAG . . . F 3 -15.187 3.291 4.458 1 85.28 ? C8 NAG 701 B 1 HETATM 9 N N2 NAG . . . F 3 -16.374 1.438 3.482 1 93.02 ? N2 NAG 701 B 1 HETATM 10 O O3 NAG . . . F 3 -19.119 2.091 3.049 1 87.24 ? O3 NAG 701 B 1 HETATM 11 O O4 NAG . . . F 3 -20.861 -0.069 2.164 1 96.6 ? O4 NAG 701 B 1 HETATM 12 O O5 NAG . . . F 3 -17.524 -1.439 1.377 1 96.43 ? O5 NAG 701 B 1 HETATM 13 O O6 NAG . . . F 3 -18.736 -2.472 -0.705 1 86.69 ? O6 NAG 701 B 1 HETATM 14 O O7 NAG . . . F 3 -16.522 3.449 2.49 1 103.48 ? O7 NAG 701 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 14 #