data_7JN5 # _model_server_result.job_id FFKsEsGi7tBLTY1vWy1jiw _model_server_result.datetime_utc '2024-10-11 09:19:42' _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 7jn5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 7JN5 # _exptl.entry_id 7JN5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _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 99.77 _cell.angle_gamma 90 _cell.entry_id 7JN5 _cell.length_a 265.736 _cell.length_b 59.931 _cell.length_c 51.721 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JN5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 A 1 NAG F 1509 NAG 4 n D NAG 2 A 2 NAG F 1510 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 22 H CYS 22 1_555 A SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 145 H CYS 139 1_555 A SG CYS 201 H CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 A SG CYS 221 H CYS 215 1_555 B SG CYS 220 L CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 B SG CYS 23 L CYS 23 1_555 B SG CYS 94 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 B SG CYS 140 L CYS 134 1_555 B SG CYS 200 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 C SG CYS 18 F CYS 323 1_555 C SG CYS 43 F CYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? disulf ? disulf7 C SG CYS 61 F CYS 366 1_555 C SG CYS 114 F CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 C SG CYS 73 F CYS 378 1_555 C SG CYS 206 F CYS 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 C SG CYS 162 F CYS 467 1_555 C SG CYS 169 F CYS 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? covale ? covale1 C ND2 ASN 25 F ASN 330 1_555 F C1 NAG . F NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale2 C ND2 ASN 52 F ASN 357 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 7JN5 _atom_sites.fract_transf_matrix[1][1] 0.003763 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000648 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016686 _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] 0.019619 _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 5 PO4 H 1 301 1 PO4 PO4 . F 6 NAG F 1 601 1511 NAG NAG . G 7 HOH H 1 401 1 HOH HOH . G 7 HOH H 2 402 2 HOH HOH . G 7 HOH H 3 403 19 HOH HOH . G 7 HOH H 4 404 13 HOH HOH . G 7 HOH H 5 405 27 HOH HOH . G 7 HOH H 6 406 25 HOH HOH . G 7 HOH H 7 407 10 HOH HOH . G 7 HOH H 8 408 8 HOH HOH . G 7 HOH H 9 409 22 HOH HOH . G 7 HOH H 10 410 28 HOH HOH . G 7 HOH H 11 411 18 HOH HOH . G 7 HOH H 12 412 26 HOH HOH . G 7 HOH H 13 413 12 HOH HOH . H 7 HOH L 1 301 20 HOH HOH . H 7 HOH L 2 302 23 HOH HOH . H 7 HOH L 3 303 11 HOH HOH . H 7 HOH L 4 304 4 HOH HOH . H 7 HOH L 5 305 6 HOH HOH . H 7 HOH L 6 306 17 HOH HOH . H 7 HOH L 7 307 5 HOH HOH . H 7 HOH L 8 308 24 HOH HOH . I 7 HOH F 1 701 16 HOH HOH . I 7 HOH F 2 702 9 HOH HOH . I 7 HOH F 3 703 29 HOH HOH . I 7 HOH F 4 704 15 HOH HOH . I 7 HOH F 5 705 7 HOH HOH . I 7 HOH F 6 706 21 HOH HOH . I 7 HOH F 7 707 3 HOH HOH . I 7 HOH F 8 708 14 HOH HOH . I 7 HOH F 9 709 30 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 . . . F 6 15.182 -47.836 -6.37 1 30 ? C1 NAG 601 F 1 HETATM 2 C C2 NAG . . . F 6 15.182 -48.513 -5.022 1 30 ? C2 NAG 601 F 1 HETATM 3 C C3 NAG . . . F 6 16.576 -48.819 -4.569 1 30 ? C3 NAG 601 F 1 HETATM 4 C C4 NAG . . . F 6 17.162 -49.705 -5.618 1 30 ? C4 NAG 601 F 1 HETATM 5 C C5 NAG . . . F 6 17.132 -49.004 -6.949 1 30 ? C5 NAG 601 F 1 HETATM 6 C C6 NAG . . . F 6 17.774 -49.89 -8 1 30 ? C6 NAG 601 F 1 HETATM 7 C C7 NAG . . . F 6 14.851 -46.461 -3.827 1 30 ? C7 NAG 601 F 1 HETATM 8 C C8 NAG . . . F 6 14.25 -45.847 -2.619 1 30 ? C8 NAG 601 F 1 HETATM 9 N N2 NAG . . . F 6 14.547 -47.708 -4.018 1 30 ? N2 NAG 601 F 1 HETATM 10 O O3 NAG . . . F 6 16.508 -49.539 -3.345 1 30 ? O3 NAG 601 F 1 HETATM 11 O O4 NAG . . . F 6 18.482 -50.102 -5.293 1 30 ? O4 NAG 601 F 1 HETATM 12 O O5 NAG . . . F 6 15.791 -48.708 -7.29 1 30 ? O5 NAG 601 F 1 HETATM 13 O O6 NAG . . . F 6 18.813 -50.688 -7.417 1 30 ? O6 NAG 601 F 1 HETATM 14 O O7 NAG . . . F 6 15.571 -45.863 -4.572 1 30 ? O7 NAG 601 F 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #