data_6BNK # _model_server_result.job_id pkynMDYzPsm71k6DuZqEQw _model_server_result.datetime_utc '2024-12-04 15:14:04' _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 6bnk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":402}' # _entry.id 6BNK # _exptl.entry_id 6BNK _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.23 _cell.angle_gamma 90 _cell.entry_id 6BNK _cell.length_a 79.97 _cell.length_b 150.57 _cell.length_c 101.2 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BNK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,K,L,M,Q,R,S,T 1 1 E,F,G,H,J,N,O,P,U,V,W,X 2 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 K N N ? 6 L N N ? 6 N N N ? 6 O N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _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 5 n I NAG 1 I 1 NAG A 511 NAG 5 n I NAG 2 I 2 NAG A 512 NAG 5 n J NAG 1 J 1 NAG E 511 NAG 5 n J NAG 2 J 2 NAG E 512 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 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 C SG CYS 22 C CYS 22 1_555 C SG CYS 89 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 C SG CYS 136 C CYS 139 1_555 C SG CYS 186 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 C SG CYS 161 C CYS 164 1_555 D SG CYS 169 D CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 D SG CYS 24 D CYS 23 1_555 D SG CYS 92 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 D SG CYS 143 D CYS 148 1_555 D SG CYS 208 D CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf9 E SG CYS 104 E CYS 104 1_555 E SG CYS 168 E CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf10 E SG CYS 208 E CYS 208 1_555 E SG CYS 263 E CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 F SG CYS 25 F CYS 25 1_555 F SG CYS 80 F CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 G SG CYS 22 G CYS 22 1_555 G SG CYS 89 G CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 G SG CYS 136 G CYS 139 1_555 G SG CYS 186 G CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf14 G SG CYS 161 G CYS 164 1_555 H SG CYS 169 H CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 H SG CYS 24 H CYS 23 1_555 H SG CYS 92 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 H SG CYS 143 H CYS 148 1_555 H SG CYS 208 H CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 K C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 L C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 E ND2 ASN 20 E ASN 20 1_555 N C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 E ND2 ASN 42 E ASN 42 1_555 O C1 NAG . E NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 E ND2 ASN 165 E ASN 165 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale8 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? # _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 396 n n C1 O1 NAG sing 397 n n C1 O5 NAG sing 398 n n C1 H1 NAG sing 399 n n C2 C3 NAG sing 400 n n C2 N2 NAG sing 401 n n C2 H2 NAG sing 402 n n C3 C4 NAG sing 403 n n C3 O3 NAG sing 404 n n C3 H3 NAG sing 405 n n C4 C5 NAG sing 406 n n C4 O4 NAG sing 407 n n C4 H4 NAG sing 408 n n C5 C6 NAG sing 409 n n C5 O5 NAG sing 410 n n C5 H5 NAG sing 411 n n C6 O6 NAG sing 412 n n C6 H61 NAG sing 413 n n C6 H62 NAG sing 414 n n C7 C8 NAG sing 415 n n C7 N2 NAG sing 416 n n C7 O7 NAG doub 417 n n C8 H81 NAG sing 418 n n C8 H82 NAG sing 419 n n C8 H83 NAG sing 420 n n N2 HN2 NAG sing 421 n n O1 HO1 NAG sing 422 n n O3 HO3 NAG sing 423 n n O4 HO4 NAG sing 424 n n O6 HO6 NAG sing 425 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 6BNK _atom_sites.fract_transf_matrix[1][1] 0.012505 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001145 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006641 _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] 0.009923 _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 6 NAG A 1 401 500 NAG NAG . L 6 NAG A 1 402 501 NAG NAG . M 7 AGH A 1 405 400 AGH AGH . N 6 NAG E 1 401 500 NAG NAG . O 6 NAG E 1 402 501 NAG NAG . P 7 AGH E 1 405 400 AGH AGH . Q 8 HOH A 1 501 15 HOH HOH . Q 8 HOH A 2 502 495 HOH HOH . Q 8 HOH A 3 503 520 HOH HOH . Q 8 HOH A 4 504 108 HOH HOH . Q 8 HOH A 5 505 543 HOH HOH . Q 8 HOH A 6 506 450 HOH HOH . Q 8 HOH A 7 507 600 HOH HOH . Q 8 HOH A 8 508 368 HOH HOH . R 8 HOH B 1 101 151 HOH HOH . R 8 HOH B 2 102 432 HOH HOH . R 8 HOH B 3 103 424 HOH HOH . R 8 HOH B 4 104 462 HOH HOH . S 8 HOH C 1 301 176 HOH HOH . S 8 HOH C 2 302 97 HOH HOH . S 8 HOH C 3 303 17 HOH HOH . S 8 HOH C 4 304 48 HOH HOH . S 8 HOH C 5 305 137 HOH HOH . S 8 HOH C 6 306 443 HOH HOH . S 8 HOH C 7 307 216 HOH HOH . S 8 HOH C 8 308 667 HOH HOH . S 8 HOH C 9 309 39 HOH HOH . S 8 HOH C 10 310 376 HOH HOH . S 8 HOH C 11 311 574 HOH HOH . T 8 HOH D 1 301 669 HOH HOH . T 8 HOH D 2 302 526 HOH HOH . T 8 HOH D 3 303 643 HOH HOH . T 8 HOH D 4 304 670 HOH HOH . T 8 HOH D 5 305 375 HOH HOH . T 8 HOH D 6 306 95 HOH HOH . T 8 HOH D 7 307 203 HOH HOH . T 8 HOH D 8 308 524 HOH HOH . T 8 HOH D 9 309 634 HOH HOH . T 8 HOH D 10 310 671 HOH HOH . T 8 HOH D 11 311 111 HOH HOH . T 8 HOH D 12 312 12 HOH HOH . T 8 HOH D 13 313 256 HOH HOH . T 8 HOH D 14 314 233 HOH HOH . T 8 HOH D 15 315 13 HOH HOH . T 8 HOH D 16 316 147 HOH HOH . T 8 HOH D 17 317 351 HOH HOH . T 8 HOH D 18 318 328 HOH HOH . T 8 HOH D 19 319 245 HOH HOH . T 8 HOH D 20 320 67 HOH HOH . T 8 HOH D 21 321 166 HOH HOH . T 8 HOH D 22 322 36 HOH HOH . T 8 HOH D 23 323 422 HOH HOH . T 8 HOH D 24 324 383 HOH HOH . T 8 HOH D 25 325 69 HOH HOH . T 8 HOH D 26 326 525 HOH HOH . T 8 HOH D 27 327 616 HOH HOH . T 8 HOH D 28 328 508 HOH HOH . T 8 HOH D 29 329 407 HOH HOH . T 8 HOH D 30 330 465 HOH HOH . T 8 HOH D 31 331 665 HOH HOH . T 8 HOH D 32 332 260 HOH HOH . U 8 HOH E 1 501 594 HOH HOH . U 8 HOH E 2 502 5 HOH HOH . U 8 HOH E 3 503 437 HOH HOH . U 8 HOH E 4 504 180 HOH HOH . U 8 HOH E 5 505 666 HOH HOH . U 8 HOH E 6 506 190 HOH HOH . U 8 HOH E 7 507 71 HOH HOH . U 8 HOH E 8 508 518 HOH HOH . V 8 HOH F 1 101 296 HOH HOH . V 8 HOH F 2 102 330 HOH HOH . W 8 HOH G 1 301 504 HOH HOH . W 8 HOH G 2 302 333 HOH HOH . W 8 HOH G 3 303 622 HOH HOH . W 8 HOH G 4 304 168 HOH HOH . W 8 HOH G 5 305 135 HOH HOH . W 8 HOH G 6 306 9 HOH HOH . W 8 HOH G 7 307 46 HOH HOH . W 8 HOH G 8 308 24 HOH HOH . W 8 HOH G 9 309 212 HOH HOH . W 8 HOH G 10 310 573 HOH HOH . W 8 HOH G 11 311 104 HOH HOH . W 8 HOH G 12 312 527 HOH HOH . W 8 HOH G 13 313 578 HOH HOH . W 8 HOH G 14 314 436 HOH HOH . X 8 HOH H 1 301 673 HOH HOH . X 8 HOH H 2 302 675 HOH HOH . X 8 HOH H 3 303 512 HOH HOH . X 8 HOH H 4 304 308 HOH HOH . X 8 HOH H 5 305 623 HOH HOH . X 8 HOH H 6 306 323 HOH HOH . X 8 HOH H 7 307 246 HOH HOH . X 8 HOH H 8 308 87 HOH HOH . X 8 HOH H 9 309 674 HOH HOH . X 8 HOH H 10 310 321 HOH HOH . X 8 HOH H 11 311 427 HOH HOH . X 8 HOH H 12 312 348 HOH HOH . X 8 HOH H 13 313 224 HOH HOH . X 8 HOH H 14 314 672 HOH HOH . X 8 HOH H 15 315 27 HOH HOH . X 8 HOH H 16 316 73 HOH HOH . X 8 HOH H 17 317 299 HOH HOH . X 8 HOH H 18 318 191 HOH HOH . X 8 HOH H 19 319 33 HOH HOH . X 8 HOH H 20 320 538 HOH HOH . X 8 HOH H 21 321 331 HOH HOH . X 8 HOH H 22 322 43 HOH HOH . X 8 HOH H 23 323 451 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 . . . O 6 19.616 -46.175 14.788 1 50.02 ? C1 NAG 402 E 1 HETATM 2 C C2 NAG . . . O 6 18.891 -45.89 13.472 1 50.82 ? C2 NAG 402 E 1 HETATM 3 C C3 NAG . . . O 6 19.933 -45.949 12.355 1 51.92 ? C3 NAG 402 E 1 HETATM 4 C C4 NAG . . . O 6 21.019 -44.903 12.584 1 51.54 ? C4 NAG 402 E 1 HETATM 5 C C5 NAG . . . O 6 21.656 -45.106 13.96 1 50.15 ? C5 NAG 402 E 1 HETATM 6 C C6 NAG . . . O 6 22.573 -43.976 14.371 1 51.33 ? C6 NAG 402 E 1 HETATM 7 C C7 NAG . . . O 6 16.52 -46.538 13.373 1 51.22 ? C7 NAG 402 E 1 HETATM 8 C C8 NAG . . . O 6 15.551 -47.59 12.925 1 51.35 ? C8 NAG 402 E 1 HETATM 9 N N2 NAG . . . O 6 17.816 -46.836 13.223 1 49.77 ? N2 NAG 402 E 1 HETATM 10 O O3 NAG . . . O 6 19.312 -45.748 11.09 1 54.69 ? O3 NAG 402 E 1 HETATM 11 O O4 NAG . . . O 6 22.007 -44.991 11.559 1 51.08 ? O4 NAG 402 E 1 HETATM 12 O O5 NAG . . . O 6 20.639 -45.19 14.979 1 49.69 ? O5 NAG 402 E 1 HETATM 13 O O6 NAG . . . O 6 21.844 -42.885 14.928 1 53.33 ? O6 NAG 402 E 1 HETATM 14 O O7 NAG . . . O 6 16.145 -45.468 13.843 1 52.97 ? O7 NAG 402 E 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #