data_3RJD # _model_server_result.job_id yaArUzGBIxb237P0H5Pd8A _model_server_result.datetime_utc '2024-12-26 23:37:00' _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 3rjd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":4}' # _entry.id 3RJD # _exptl.entry_id 3RJD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 3RJD _cell.length_a 92.828 _cell.length_b 92.828 _cell.length_c 90.763 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RJD _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 G N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide 5 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 5 ? 3 4 1 FUC NAG C1 O1 . O6 HO6 . sing 6 ? 4 2 1 MAN NAG C1 O1 . O4 HO4 . sing 7 ? 5 2 1 NAG 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 2 n B NAG 1 B 1 NAG S 242 NAG 2 n B NAG 2 B 2 NAG S 243 NAG 2 n B MAN 3 B 3 MAN A 285 MAN 3 n C NAG 1 C 1 NAG S 10 NAG 3 n C NAG 2 C 2 NAG A 11 NAG 3 n C MAN 3 C 3 MAN A 12 MAN 3 n C FUC 4 C 4 FUC D 999 FUC 4 n D NAG 1 D 1 NAG C 367 NAG 4 n D MAN 2 D 2 MAN C 368 MAN 5 n E NAG 1 E 1 NAG B 366 NAG 5 n E NAG 2 E 2 NAG B 369 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 23 A CYS 43 1_555 A SG CYS 65 A CYS 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 104 A CYS 124 1_555 A SG CYS 148 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 192 A CYS 212 1_555 A SG CYS 240 A CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 F C1 NAG . A NAG 4 1_555 A ND2 ASN 58 A ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale2 G C1 NAG . A NAG 8 1_555 A ND2 ASN 175 A ASN 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale3 A ND2 ASN 39 A ASN 59 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 A ND2 ASN 132 A ASN 152 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 A ND2 ASN 139 A ASN 159 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale6 A ND2 ASN 143 A ASN 163 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale7 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 B O4 NAG . B NAG 2 1_555 B C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.556 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale10 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale11 C O4 NAG . C NAG 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale12 D O4 NAG . D NAG 1 1_555 D C1 MAN . D MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? # _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 284 n n C1 O1 NAG sing 285 n n C1 O5 NAG sing 286 n n C1 H1 NAG sing 287 n n C2 C3 NAG sing 288 n n C2 N2 NAG sing 289 n n C2 H2 NAG sing 290 n n C3 C4 NAG sing 291 n n C3 O3 NAG sing 292 n n C3 H3 NAG sing 293 n n C4 C5 NAG sing 294 n n C4 O4 NAG sing 295 n n C4 H4 NAG sing 296 n n C5 C6 NAG sing 297 n n C5 O5 NAG sing 298 n n C5 H5 NAG sing 299 n n C6 O6 NAG sing 300 n n C6 H61 NAG sing 301 n n C6 H62 NAG sing 302 n n C7 C8 NAG sing 303 n n C7 N2 NAG sing 304 n n C7 O7 NAG doub 305 n n C8 H81 NAG sing 306 n n C8 H82 NAG sing 307 n n C8 H83 NAG sing 308 n n N2 HN2 NAG sing 309 n n O1 HO1 NAG sing 310 n n O3 HO3 NAG sing 311 n n O4 HO4 NAG sing 312 n n O6 HO6 NAG sing 313 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 3RJD _atom_sites.fract_transf_matrix[1][1] 0.010773 _atom_sites.fract_transf_matrix[1][2] 0.00622 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012439 _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] 0.011018 _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 F 6 NAG A 1 4 4 NAG NAG . G 6 NAG A 1 8 8 NAG NAG . H 7 P33 A 1 1 1 P33 15P . I 8 HOH A 1 2 2 HOH HOH . I 8 HOH A 2 3 3 HOH HOH . I 8 HOH A 3 5 5 HOH HOH . I 8 HOH A 4 6 6 HOH HOH . I 8 HOH A 5 7 7 HOH HOH . I 8 HOH A 6 9 9 HOH HOH . I 8 HOH A 7 14 14 HOH HOH . I 8 HOH A 8 15 15 HOH HOH . I 8 HOH A 9 17 17 HOH HOH . I 8 HOH A 10 18 18 HOH HOH . I 8 HOH A 11 19 19 HOH HOH . I 8 HOH A 12 286 1 HOH HOH . I 8 HOH A 13 287 4 HOH HOH . I 8 HOH A 14 288 8 HOH HOH . I 8 HOH A 15 289 10 HOH HOH . I 8 HOH A 16 290 11 HOH HOH . I 8 HOH A 17 291 12 HOH HOH . I 8 HOH A 18 292 21 HOH HOH . I 8 HOH A 19 293 22 HOH HOH . I 8 HOH A 20 294 23 HOH HOH . I 8 HOH A 21 295 24 HOH HOH . I 8 HOH A 22 296 25 HOH HOH . I 8 HOH A 23 297 26 HOH HOH . I 8 HOH A 24 298 27 HOH HOH . I 8 HOH A 25 299 28 HOH HOH . I 8 HOH A 26 300 29 HOH HOH . I 8 HOH A 27 301 31 HOH HOH . I 8 HOH A 28 302 32 HOH HOH . I 8 HOH A 29 303 33 HOH HOH . I 8 HOH A 30 304 34 HOH HOH . I 8 HOH A 31 305 36 HOH HOH . I 8 HOH A 32 306 37 HOH HOH . I 8 HOH A 33 307 38 HOH HOH . I 8 HOH A 34 308 39 HOH HOH . I 8 HOH A 35 309 40 HOH HOH . I 8 HOH A 36 310 41 HOH HOH . I 8 HOH A 37 311 42 HOH HOH . I 8 HOH A 38 312 43 HOH HOH . I 8 HOH A 39 313 44 HOH HOH . I 8 HOH A 40 314 45 HOH HOH . I 8 HOH A 41 315 46 HOH HOH . I 8 HOH A 42 316 47 HOH HOH . I 8 HOH A 43 317 49 HOH HOH . I 8 HOH A 44 318 50 HOH HOH . I 8 HOH A 45 319 51 HOH HOH . I 8 HOH A 46 320 52 HOH HOH . I 8 HOH A 47 321 53 HOH HOH . I 8 HOH A 48 322 54 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 12.638 26.164 3.494 1 115.54 ? C1 NAG 4 A 1 HETATM 2 C C2 NAG . . . F 6 13.925 25.289 3.558 1 119 ? C2 NAG 4 A 1 HETATM 3 C C3 NAG . . . F 6 14.972 25.93 4.531 1 121.63 ? C3 NAG 4 A 1 HETATM 4 C C4 NAG . . . F 6 15.159 27.468 4.34 1 122.26 ? C4 NAG 4 A 1 HETATM 5 C C5 NAG . . . F 6 13.779 28.175 4.221 1 119.68 ? C5 NAG 4 A 1 HETATM 6 C C6 NAG . . . F 6 13.908 29.679 3.897 1 121.04 ? C6 NAG 4 A 1 HETATM 7 C C7 NAG . . . F 6 13.331 22.899 3.055 1 121.29 ? C7 NAG 4 A 1 HETATM 8 C C8 NAG . . . F 6 12.959 21.591 3.7 1 122.08 ? C8 NAG 4 A 1 HETATM 9 N N2 NAG . . . F 6 13.555 23.92 3.952 1 119.81 ? N2 NAG 4 A 1 HETATM 10 O O3 NAG . . . F 6 16.245 25.248 4.412 1 125.61 ? O3 NAG 4 A 1 HETATM 11 O O4 NAG . . . F 6 15.888 28.018 5.467 1 125.62 ? O4 NAG 4 A 1 HETATM 12 O O5 NAG . . . F 6 12.927 27.544 3.228 1 117.09 ? O5 NAG 4 A 1 HETATM 13 O O6 NAG . . . F 6 14.153 29.941 2.505 1 123.51 ? O6 NAG 4 A 1 HETATM 14 O O7 NAG . . . F 6 13.423 23.028 1.835 1 123.41 ? O7 NAG 4 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 14 #