data_4DJ7 # _model_server_result.job_id etA5HtyfLk0VBoqjqfjPVg _model_server_result.datetime_utc '2024-11-23 21:22:02' _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 4dj7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":401}' # _entry.id 4DJ7 # _exptl.entry_id 4DJ7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 11 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 124.39 _cell.angle_gamma 90 _cell.entry_id 4DJ7 _cell.length_a 200.279 _cell.length_b 115.723 _cell.length_c 117.656 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DJ7 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA _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 ? 5 K N N ? 5 L N N ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T N N ? 5 U N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 4 2 1 GAL NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 SIA GAL C2 O2 . O3 HO3 . 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 G NAG 1 G 1 NAG I 1 NAG 3 n G NAG 2 G 2 NAG I 2 NAG 4 n H NAG 1 H 1 NAG Y 3 NAG 4 n H GAL 2 H 2 GAL Y 2 GAL 4 n H SIA 3 H 3 SIA Y 1 SIA 4 n I NAG 1 I 1 NAG Z 3 NAG 4 n I GAL 2 I 2 GAL Z 2 GAL 4 n I SIA 3 I 3 SIA Z 1 SIA 4 n J NAG 1 J 1 NAG X 3 NAG 4 n J GAL 2 J 2 GAL X 2 GAL 4 n J SIA 3 J 3 SIA X 1 SIA # 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 8 A CYS 4 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 46 A CYS 42 1_555 A SG CYS 272 A CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf3 A SG CYS 58 A CYS 54 1_555 A SG CYS 70 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf4 A SG CYS 91 A CYS 87 1_555 A SG CYS 133 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf5 A SG CYS 276 A CYS 273 1_555 A SG CYS 300 A CYS 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 C SG CYS 8 C CYS 4 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 46 C CYS 42 1_555 C SG CYS 272 C CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf9 C SG CYS 58 C CYS 54 1_555 C SG CYS 70 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf10 C SG CYS 91 C CYS 87 1_555 C SG CYS 133 C CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf11 C SG CYS 276 C CYS 273 1_555 C SG CYS 300 C CYS 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 E SG CYS 8 E CYS 4 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 E SG CYS 46 E CYS 42 1_555 E SG CYS 272 E CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf15 E SG CYS 58 E CYS 54 1_555 E SG CYS 70 E CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf16 E SG CYS 91 E CYS 87 1_555 E SG CYS 133 E CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf17 E SG CYS 276 E CYS 273 1_555 E SG CYS 300 E CYS 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 32 A ASN 28 1_555 K C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 127 A ASN 123 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale3 A ND2 ASN 235 A ASN 231 1_555 L C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale4 B ND2 ASN 82 B ASN 82 1_555 M C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 C ND2 ASN 32 C ASN 28 1_555 O C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale6 C ND2 ASN 127 C ASN 123 1_555 N C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 C ND2 ASN 235 C ASN 231 1_555 P C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 D ND2 ASN 82 D ASN 82 1_555 Q C1 NAG . D NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 E ND2 ASN 32 E ASN 28 1_555 S C1 NAG . E NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale10 E ND2 ASN 127 E ASN 123 1_555 R C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 E ND2 ASN 235 E ASN 231 1_555 T C1 NAG . E NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 F ND2 ASN 82 F ASN 82 1_555 U C1 NAG . F NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale14 H O4 NAG . H NAG 1 1_555 H C1 GAL . H GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale15 H O3 GAL . H GAL 2 1_555 H C2 SIA . H SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale16 I O4 NAG . I NAG 1 1_555 I C1 GAL . I GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale17 I O3 GAL . I GAL 2 1_555 I C2 SIA . I SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale18 J O4 NAG . J NAG 1 1_555 J C1 GAL . J GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale19 J O3 GAL . J GAL 2 1_555 J C2 SIA . J SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? # _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 4DJ7 _atom_sites.fract_transf_matrix[1][1] 0.004993 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003417 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008641 _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] 0.010299 _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 K 5 NAG A 1 403 1 NAG NAG . L 5 NAG A 1 404 1 NAG NAG . M 5 NAG B 1 201 1 NAG NAG . N 5 NAG C 1 401 1 NAG NAG . O 5 NAG C 1 402 1 NAG NAG . P 5 NAG C 1 403 1 NAG NAG . Q 5 NAG D 1 201 1 NAG NAG . R 5 NAG E 1 401 1 NAG NAG . S 5 NAG E 1 402 1 NAG NAG . T 5 NAG E 1 403 1 NAG NAG . U 5 NAG F 1 201 1 NAG NAG . V 6 HOH A 1 501 2 HOH HOH . V 6 HOH A 2 502 22 HOH HOH . V 6 HOH A 3 503 47 HOH HOH . W 6 HOH B 1 301 5 HOH HOH . W 6 HOH B 2 302 8 HOH HOH . W 6 HOH B 3 303 14 HOH HOH . W 6 HOH B 4 304 42 HOH HOH . X 6 HOH C 1 501 7 HOH HOH . X 6 HOH C 2 502 17 HOH HOH . X 6 HOH C 3 503 21 HOH HOH . X 6 HOH C 4 504 23 HOH HOH . X 6 HOH C 5 505 24 HOH HOH . X 6 HOH C 6 506 25 HOH HOH . X 6 HOH C 7 507 33 HOH HOH . Y 6 HOH D 1 301 6 HOH HOH . Y 6 HOH D 2 302 9 HOH HOH . Y 6 HOH D 3 303 11 HOH HOH . Y 6 HOH D 4 304 38 HOH HOH . Y 6 HOH D 5 305 40 HOH HOH . Z 6 HOH E 1 501 13 HOH HOH . Z 6 HOH E 2 502 26 HOH HOH . Z 6 HOH E 3 503 27 HOH HOH . Z 6 HOH E 4 504 43 HOH HOH . Z 6 HOH E 5 505 48 HOH HOH . Z 6 HOH E 6 506 49 HOH HOH . AA 6 HOH F 1 301 3 HOH HOH . AA 6 HOH F 2 302 10 HOH HOH . AA 6 HOH F 3 303 16 HOH HOH . AA 6 HOH F 4 304 20 HOH HOH . AA 6 HOH F 5 305 44 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 . . . R 5 18.203 -35.75 89.423 1 151.12 ? C1 NAG 401 E 1 HETATM 2 C C2 NAG . . . R 5 16.992 -36.323 90.164 1 173.33 ? C2 NAG 401 E 1 HETATM 3 C C3 NAG . . . R 5 17.206 -36.532 91.673 1 186.67 ? C3 NAG 401 E 1 HETATM 4 C C4 NAG . . . R 5 18.599 -37.082 91.978 1 187.92 ? C4 NAG 401 E 1 HETATM 5 C C5 NAG . . . R 5 19.597 -36.168 91.275 1 177.09 ? C5 NAG 401 E 1 HETATM 6 C C6 NAG . . . R 5 21.057 -36.362 91.698 1 175.63 ? C6 NAG 401 E 1 HETATM 7 C C7 NAG . . . R 5 14.832 -35.914 89.136 1 178.99 ? C7 NAG 401 E 1 HETATM 8 C C8 NAG . . . R 5 13.657 -34.981 88.986 1 162.94 ? C8 NAG 401 E 1 HETATM 9 N N2 NAG . . . R 5 15.825 -35.494 89.924 1 167.78 ? N2 NAG 401 E 1 HETATM 10 O O3 NAG . . . R 5 16.233 -37.417 92.189 1 191.47 ? O3 NAG 401 E 1 HETATM 11 O O4 NAG . . . R 5 18.834 -37.18 93.374 1 189.11 ? O4 NAG 401 E 1 HETATM 12 O O5 NAG . . . R 5 19.405 -36.346 89.886 1 166.22 ? O5 NAG 401 E 1 HETATM 13 O O6 NAG . . . R 5 21.583 -37.579 91.218 1 163.54 ? O6 NAG 401 E 1 HETATM 14 O O7 NAG . . . R 5 14.859 -37.006 88.555 1 168.23 ? O7 NAG 401 E 1 # _model_server_stats.io_time_ms 87 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #