data_5J06 # _model_server_result.job_id 9wFrk4AindGZjZLjwB5_lw _model_server_result.datetime_utc '2024-11-12 21:17:01' _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 5j06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":301}' # _entry.id 5J06 # _exptl.entry_id 5J06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 13 _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 5J06 _cell.length_a 65.05 _cell.length_b 127.06 _cell.length_c 142.83 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5J06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,F,G,H,R,S,T,U,V,Y 1 1 C,N,O,P,Q,X 2 1 B,E,I,J,K,L,M,W 2 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_445 x-1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 -32.525 -63.53 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 R N N ? 3 S N N ? 3 T 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 SIA _pdbx_entity_branch_link.comp_id_2 GAL _pdbx_entity_branch_link.atom_id_1 C2 _pdbx_entity_branch_link.leaving_atom_id_1 O2 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _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 E GAL 1 E 1 GAL B 8301 GAL 2 n E SIA 2 E 2 SIA B 8300 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 19 A CYS 36 1_555 A SG CYS 152 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 24 A CYS 41 1_555 A SG CYS 84 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 146 A CYS 163 1_555 A SG CYS 195 A CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 19 B CYS 36 1_555 B SG CYS 152 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 B SG CYS 24 B CYS 41 1_555 B SG CYS 84 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 B SG CYS 146 B CYS 163 1_555 B SG CYS 195 B CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 C SG CYS 19 C CYS 36 1_555 C SG CYS 152 C CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 C SG CYS 24 C CYS 41 1_555 C SG CYS 84 C CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 146 C CYS 163 1_555 C SG CYS 195 C CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 D SG CYS 19 D CYS 36 1_555 D SG CYS 152 D CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf11 D SG CYS 24 D CYS 41 1_555 D SG CYS 84 D CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 D SG CYS 146 D CYS 163 1_555 D SG CYS 195 D CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 83 A ASN 100 1_555 F C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 143 A ASN 160 1_555 G C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 A ND2 ASN 192 A ASN 209 1_555 H C1 NAG . A NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 B ND2 ASN 83 B ASN 100 1_555 I C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 B ND2 ASN 143 B ASN 160 1_555 J C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 B ND2 ASN 192 B ASN 209 1_555 K C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 B ND2 ASN 213 B ASN 230 1_555 L C1 NAG . B NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale8 C ND2 ASN 83 C ASN 100 1_555 N C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 C ND2 ASN 143 C ASN 160 1_555 O C1 NAG . C NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale10 C ND2 ASN 192 C ASN 209 1_555 P C1 NAG . C NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 D ND2 ASN 83 D ASN 100 1_555 R C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale12 D ND2 ASN 143 D ASN 160 1_555 S C1 NAG . D NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale13 D ND2 ASN 192 D ASN 209 1_555 T C1 NAG . D NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale14 E O3 GAL . E GAL 1 1_555 E C2 SIA . E SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? # _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 5J06 _atom_sites.fract_transf_matrix[1][1] 0.015373 _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] 0.00787 _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] 0.007001 _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 3 NAG A 1 301 9100 NAG NAG . G 3 NAG A 1 302 9160 NAG NAG . H 3 NAG A 1 303 9209 NAG NAG . I 3 NAG B 1 301 8100 NAG NAG . J 3 NAG B 1 302 8160 NAG NAG . K 3 NAG B 1 303 8209 NAG NAG . L 3 NAG B 1 304 8230 NAG NAG . M 4 PG0 B 1 307 8400 PG0 PG0 . N 3 NAG C 1 301 7100 NAG NAG . O 3 NAG C 1 302 7160 NAG NAG . P 3 NAG C 1 303 7209 NAG NAG . Q 4 PG0 C 1 304 7400 PG0 PG0 . R 3 NAG D 1 301 6100 NAG NAG . S 3 NAG D 1 302 6160 NAG NAG . T 3 NAG D 1 303 6209 NAG NAG . U 5 SIA D 1 304 6300 SIA SIA . V 6 HOH A 1 401 30 HOH HOH . V 6 HOH A 2 402 3 HOH HOH . V 6 HOH A 3 403 39 HOH HOH . V 6 HOH A 4 404 36 HOH HOH . V 6 HOH A 5 405 5 HOH HOH . V 6 HOH A 6 406 48 HOH HOH . V 6 HOH A 7 407 2 HOH HOH . V 6 HOH A 8 408 13 HOH HOH . V 6 HOH A 9 409 6 HOH HOH . V 6 HOH A 10 410 16 HOH HOH . W 6 HOH B 1 401 43 HOH HOH . W 6 HOH B 2 402 8 HOH HOH . W 6 HOH B 3 403 27 HOH HOH . W 6 HOH B 4 404 1 HOH HOH . W 6 HOH B 5 405 15 HOH HOH . W 6 HOH B 6 406 29 HOH HOH . W 6 HOH B 7 407 7 HOH HOH . W 6 HOH B 8 408 9 HOH HOH . W 6 HOH B 9 409 46 HOH HOH . W 6 HOH B 10 410 11 HOH HOH . W 6 HOH B 11 411 21 HOH HOH . W 6 HOH B 12 412 26 HOH HOH . W 6 HOH B 13 413 22 HOH HOH . W 6 HOH B 14 414 25 HOH HOH . X 6 HOH C 1 401 12 HOH HOH . X 6 HOH C 2 402 20 HOH HOH . X 6 HOH C 3 403 32 HOH HOH . X 6 HOH C 4 404 17 HOH HOH . Y 6 HOH D 1 401 33 HOH HOH . Y 6 HOH D 2 402 4 HOH HOH . Y 6 HOH D 3 403 28 HOH HOH . Y 6 HOH D 4 404 23 HOH HOH . Y 6 HOH D 5 405 34 HOH HOH . Y 6 HOH D 6 406 19 HOH HOH . Y 6 HOH D 7 407 44 HOH HOH . Y 6 HOH D 8 408 47 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 3 -46.803 15.755 10.624 1 75.37 ? C1 NAG 301 D 1 HETATM 2 C C2 NAG . . . R 3 -48.166 16.214 10.122 1 88.64 ? C2 NAG 301 D 1 HETATM 3 C C3 NAG . . . R 3 -48.184 16.227 8.598 1 91 ? C3 NAG 301 D 1 HETATM 4 C C4 NAG . . . R 3 -47.023 17.055 8.061 1 87.5 ? C4 NAG 301 D 1 HETATM 5 C C5 NAG . . . R 3 -45.701 16.611 8.686 1 80.76 ? C5 NAG 301 D 1 HETATM 6 C C6 NAG . . . R 3 -44.554 17.529 8.335 1 82.28 ? C6 NAG 301 D 1 HETATM 7 C C7 NAG . . . R 3 -49.811 15.576 11.829 1 90.96 ? C7 NAG 301 D 1 HETATM 8 C C8 NAG . . . R 3 -50.896 14.612 12.206 1 91.73 ? C8 NAG 301 D 1 HETATM 9 N N2 NAG . . . R 3 -49.232 15.371 10.641 1 91.1 ? N2 NAG 301 D 1 HETATM 10 O O3 NAG . . . R 3 -49.419 16.772 8.146 1 96.58 ? O3 NAG 301 D 1 HETATM 11 O O4 NAG . . . R 3 -46.936 16.902 6.649 1 85.63 ? O4 NAG 301 D 1 HETATM 12 O O5 NAG . . . R 3 -45.798 16.614 10.118 1 74.86 ? O5 NAG 301 D 1 HETATM 13 O O6 NAG . . . R 3 -43.397 17.228 9.102 1 98.08 ? O6 NAG 301 D 1 HETATM 14 O O7 NAG . . . R 3 -49.473 16.497 12.567 1 90.11 ? O7 NAG 301 D 1 HETATM 15 H H1 NAG . . . R 3 -46.635 14.845 10.313 1 90.45 ? H1 NAG 301 D 1 HETATM 16 H H2 NAG . . . R 3 -48.314 17.128 10.432 1 106.36 ? H2 NAG 301 D 1 HETATM 17 H H3 NAG . . . R 3 -48.101 15.311 8.271 1 109.2 ? H3 NAG 301 D 1 HETATM 18 H H4 NAG . . . R 3 -47.177 17.995 8.272 1 105 ? H4 NAG 301 D 1 HETATM 19 H H5 NAG . . . R 3 -45.492 15.708 8.382 1 96.91 ? H5 NAG 301 D 1 HETATM 20 H H61 NAG . . . R 3 -44.82 18.452 8.507 1 98.74 ? H61 NAG 301 D 1 HETATM 21 H H62 NAG . . . R 3 -44.344 17.428 7.388 1 98.74 ? H62 NAG 301 D 1 HETATM 22 H H81 NAG . . . R 3 -50.531 13.707 12.235 1 110.08 ? H81 NAG 301 D 1 HETATM 23 H H82 NAG . . . R 3 -51.612 14.653 11.545 1 110.08 ? H82 NAG 301 D 1 HETATM 24 H H83 NAG . . . R 3 -51.25 14.848 13.084 1 110.08 ? H83 NAG 301 D 1 HETATM 25 H HN2 NAG . . . R 3 -49.521 14.673 10.13 1 109.32 ? HN2 NAG 301 D 1 HETATM 26 H HO3 NAG . . . R 3 -49.41 16.832 7.26 1 115.89 ? HO3 NAG 301 D 1 HETATM 27 H HO4 NAG . . . R 3 -46.456 17.567 6.308 1 102.75 ? HO4 NAG 301 D 1 HETATM 28 H HO6 NAG . . . R 3 -42.705 17.685 8.785 1 117.69 ? HO6 NAG 301 D 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #