data_4KTH # _model_server_result.job_id mS4btKXlQ78NGESIaciSmw _model_server_result.datetime_utc '2024-11-26 20:06:36' _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 4kth # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":403}' # _entry.id 4KTH # _exptl.entry_id 4KTH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 121.66 _cell.angle_gamma 90 _cell.entry_id 4KTH _cell.length_a 174.121 _cell.length_b 101.585 _cell.length_c 124.928 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KTH _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression C,E,F,I,Q,T,V,W 1 1 A,B,D,G,H,J,K,L,M,N,O,P,R,S,U 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W 3 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 ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 3 n G NAG 1 G 1 NAG A 323 NAG 3 n G NAG 2 G 2 NAG A 324 NAG 3 n H NAG 1 H 1 NAG A 328 NAG 3 n H NAG 2 H 2 NAG A 329 NAG 3 n I NAG 1 I 1 NAG B 176 NAG 3 n I NAG 2 I 2 NAG B 177 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 8 A CYS 4 1_555 C SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 46 A CYS 42 1_555 A SG CYS 278 A CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 59 A CYS 55 1_555 A SG CYS 71 A CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 94 A CYS 90 1_555 A SG CYS 139 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf5 A SG CYS 282 A CYS 278 1_555 A SG CYS 306 A CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 B SG CYS 8 E CYS 4 1_555 E SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf7 B SG CYS 46 E CYS 42 1_555 B SG CYS 278 E CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf8 B SG CYS 59 E CYS 55 1_555 B SG CYS 71 E CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 94 E CYS 90 1_555 B SG CYS 139 E CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf10 B SG CYS 282 E CYS 278 1_555 B SG CYS 306 E CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf11 C SG CYS 144 B CYS 144 1_555 C SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 D SG CYS 8 C CYS 4 1_555 F SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf13 D SG CYS 46 C CYS 42 1_555 D SG CYS 278 C CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf14 D SG CYS 59 C CYS 55 1_555 D SG CYS 71 C CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf15 D SG CYS 94 C CYS 90 1_555 D SG CYS 139 C CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf16 D SG CYS 282 C CYS 278 1_555 D SG CYS 306 C CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf17 E SG CYS 144 F CYS 144 1_555 E SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf18 F SG CYS 144 D CYS 144 1_555 F SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A ND2 ASN 15 A ASN 11 1_555 K C1 NAG . A NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 27 A ASN 23 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 169 A ASN 165 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 A ND2 ASN 290 A ASN 286 1_555 J C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 B ND2 ASN 27 E ASN 23 1_555 M C1 NAG . E NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale6 B ND2 ASN 169 E ASN 165 1_555 L C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 C ND2 ASN 154 B ASN 154 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 D ND2 ASN 15 C ASN 11 1_555 P C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 D ND2 ASN 27 C ASN 23 1_555 O C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 D ND2 ASN 169 C ASN 165 1_555 N C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale11 E ND2 ASN 154 F ASN 154 1_555 Q C1 NAG . F NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale12 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale14 I O4 NAG . I NAG 1 1_555 I C1 NAG . I 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 4KTH _atom_sites.fract_transf_matrix[1][1] 0.005743 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003542 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009844 _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] 0.009405 _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 J 4 NAG A 1 401 322 NAG NAG . K 4 NAG A 1 406 330 NAG NAG . L 4 NAG E 1 401 323 NAG NAG . M 4 NAG E 1 402 324 NAG NAG . N 4 NAG C 1 401 326 NAG NAG . O 4 NAG C 1 402 327 NAG NAG . P 4 NAG C 1 403 328 NAG NAG . Q 4 NAG F 1 201 176 NAG NAG . R 5 HOH A 1 501 3 HOH HOH . R 5 HOH A 2 502 5 HOH HOH . R 5 HOH A 3 503 7 HOH HOH . R 5 HOH A 4 504 8 HOH HOH . R 5 HOH A 5 505 13 HOH HOH . R 5 HOH A 6 506 23 HOH HOH . R 5 HOH A 7 507 26 HOH HOH . R 5 HOH A 8 508 28 HOH HOH . R 5 HOH A 9 509 33 HOH HOH . R 5 HOH A 10 510 143 HOH HOH . R 5 HOH A 11 511 148 HOH HOH . R 5 HOH A 12 512 149 HOH HOH . R 5 HOH A 13 513 154 HOH HOH . R 5 HOH A 14 514 160 HOH HOH . R 5 HOH A 15 515 181 HOH HOH . R 5 HOH A 16 516 182 HOH HOH . R 5 HOH A 17 517 183 HOH HOH . R 5 HOH A 18 518 185 HOH HOH . R 5 HOH A 19 519 186 HOH HOH . R 5 HOH A 20 520 212 HOH HOH . R 5 HOH A 21 521 213 HOH HOH . R 5 HOH A 22 522 214 HOH HOH . R 5 HOH A 23 523 216 HOH HOH . S 5 HOH E 1 501 9 HOH HOH . S 5 HOH E 2 502 19 HOH HOH . S 5 HOH E 3 503 20 HOH HOH . S 5 HOH E 4 504 34 HOH HOH . S 5 HOH E 5 505 155 HOH HOH . S 5 HOH E 6 506 165 HOH HOH . S 5 HOH E 7 507 167 HOH HOH . S 5 HOH E 8 508 170 HOH HOH . S 5 HOH E 9 509 171 HOH HOH . S 5 HOH E 10 510 203 HOH HOH . S 5 HOH E 11 511 204 HOH HOH . S 5 HOH E 12 512 205 HOH HOH . S 5 HOH E 13 513 206 HOH HOH . T 5 HOH B 1 301 4 HOH HOH . T 5 HOH B 2 302 24 HOH HOH . T 5 HOH B 3 303 35 HOH HOH . T 5 HOH B 4 304 144 HOH HOH . T 5 HOH B 5 305 168 HOH HOH . T 5 HOH B 6 306 207 HOH HOH . T 5 HOH B 7 307 217 HOH HOH . U 5 HOH C 1 501 10 HOH HOH . U 5 HOH C 2 502 15 HOH HOH . U 5 HOH C 3 503 18 HOH HOH . U 5 HOH C 4 504 21 HOH HOH . U 5 HOH C 5 505 22 HOH HOH . U 5 HOH C 6 506 31 HOH HOH . U 5 HOH C 7 507 32 HOH HOH . U 5 HOH C 8 508 37 HOH HOH . U 5 HOH C 9 509 38 HOH HOH . U 5 HOH C 10 510 39 HOH HOH . U 5 HOH C 11 511 153 HOH HOH . U 5 HOH C 12 512 175 HOH HOH . U 5 HOH C 13 513 188 HOH HOH . U 5 HOH C 14 514 189 HOH HOH . U 5 HOH C 15 515 208 HOH HOH . U 5 HOH C 16 516 209 HOH HOH . U 5 HOH C 17 517 215 HOH HOH . V 5 HOH F 1 301 14 HOH HOH . V 5 HOH F 2 302 36 HOH HOH . V 5 HOH F 3 303 190 HOH HOH . V 5 HOH F 4 304 191 HOH HOH . V 5 HOH F 5 305 192 HOH HOH . V 5 HOH F 6 306 211 HOH HOH . W 5 HOH D 1 201 27 HOH HOH . W 5 HOH D 2 202 164 HOH HOH . W 5 HOH D 3 203 179 HOH HOH . W 5 HOH D 4 204 199 HOH HOH . W 5 HOH D 5 205 218 HOH HOH . W 5 HOH D 6 206 219 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 . . . P 4 -18.109 32.861 -4.428 1 88.51 ? C1 NAG 403 C 1 HETATM 2 C C2 NAG . . . P 4 -18.48 34.33 -4.093 1 94.66 ? C2 NAG 403 C 1 HETATM 3 C C3 NAG . . . P 4 -17.436 35.378 -4.482 1 96.89 ? C3 NAG 403 C 1 HETATM 4 C C4 NAG . . . P 4 -16.032 34.85 -4.251 1 95.87 ? C4 NAG 403 C 1 HETATM 5 C C5 NAG . . . P 4 -15.836 33.594 -5.089 1 100 ? C5 NAG 403 C 1 HETATM 6 C C6 NAG . . . P 4 -14.418 33.048 -4.918 1 107.2 ? C6 NAG 403 C 1 HETATM 7 C C7 NAG . . . P 4 -20.674 35.468 -4.01 1 115.86 ? C7 NAG 403 C 1 HETATM 8 C C8 NAG . . . P 4 -21.973 35.723 -4.725 1 98.96 ? C8 NAG 403 C 1 HETATM 9 N N2 NAG . . . P 4 -19.791 34.68 -4.64 1 110.93 ? N2 NAG 403 C 1 HETATM 10 O O3 NAG . . . P 4 -17.618 36.555 -3.72 1 93.1 ? O3 NAG 403 C 1 HETATM 11 O O4 NAG . . . P 4 -15.085 35.839 -4.604 1 85.83 ? O4 NAG 403 C 1 HETATM 12 O O5 NAG . . . P 4 -16.742 32.574 -4.709 1 90.82 ? O5 NAG 403 C 1 HETATM 13 O O6 NAG . . . P 4 -13.536 33.633 -5.851 1 104.49 ? O6 NAG 403 C 1 HETATM 14 O O7 NAG . . . P 4 -20.478 35.98 -2.906 1 117.66 ? O7 NAG 403 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 14 #