data_5K33 # _model_server_result.job_id s_0KNVSA-EmKt2y0vsmuvg _model_server_result.datetime_utc '2024-11-25 15:58:32' _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 5k33 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":705}' # _entry.id 5K33 # _exptl.entry_id 5K33 _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 5K33 _cell.length_a 108.62 _cell.length_b 108.62 _cell.length_c 174.34 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K33 _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 ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 1 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_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 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 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 4 4 3 MAN BMA C1 O1 . 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 C NAG 1 B 1 NAG A 500 NAG 3 n C NAG 2 B 2 NAG A 501 NAG 3 n C BMA 3 B 3 BMA A 502 BMA 3 n C MAN 4 B 4 MAN A 506 MAN 3 n C MAN 5 B 5 MAN A 503 MAN 4 n D NAG 1 D 1 NAG C 583 NAG 4 n D NAG 2 D 2 NAG C 584 NAG 4 n D BMA 3 D 3 BMA C 585 BMA 4 n D MAN 4 D 4 MAN C 586 MAN # 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 37 A CYS 261 1_555 A SG CYS 97 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 143 A CYS 367 1_555 A SG CYS 206 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 4 C CYS 4 1_555 B SG CYS 31 C CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 B SG CYS 140 C CYS 140 1_555 B SG CYS 170 C CYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 B SG CYS 173 C CYS 173 1_555 B SG CYS 182 C CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 177 C CYS 177 1_555 B SG CYS 190 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 B SG CYS 198 C CYS 198 1_555 B SG CYS 205 C CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 B SG CYS 202 C CYS 202 1_555 B SG CYS 213 C CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 214 C CYS 214 1_555 B SG CYS 222 C CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 B SG CYS 218 C CYS 218 1_555 B SG CYS 230 C CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 B SG CYS 233 C CYS 233 1_555 B SG CYS 242 C CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 B SG CYS 246 C CYS 246 1_555 B SG CYS 273 C CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 B SG CYS 277 C CYS 277 1_555 B SG CYS 289 C CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf14 B SG CYS 293 C CYS 293 1_555 B SG CYS 309 C CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 B SG CYS 312 C CYS 312 1_555 B SG CYS 316 C CYS 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 B SG CYS 320 C CYS 320 1_555 B SG CYS 345 C CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf17 B SG CYS 453 C CYS 453 1_555 B SG CYS 482 C CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf18 B SG CYS 489 C CYS 489 1_555 B SG CYS 498 C CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf19 B SG CYS 493 C CYS 493 1_555 B SG CYS 506 C CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf20 B SG CYS 509 C CYS 509 1_555 B SG CYS 518 C CYS 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf21 B SG CYS 522 C CYS 522 1_555 B SG CYS 538 C CYS 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf22 B SG CYS 541 C CYS 541 1_555 B SG CYS 554 C CYS 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf23 B SG CYS 545 C CYS 545 1_555 B SG CYS 562 C CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf24 B SG CYS 565 C CYS 565 1_555 B SG CYS 574 C CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 73 A ASN 297 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 B ND2 ASN 165 C ASN 165 1_555 G C1 NAG . C NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 B ND2 ASN 237 C ASN 237 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 B ND2 ASN 549 C ASN 549 1_555 F C1 NAG . C NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 C O4 NAG . B NAG 2 1_555 C C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 C O3 BMA . B BMA 3 1_555 C C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale8 C O6 BMA . B BMA 3 1_555 C C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _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 296 n n C1 O1 NAG sing 297 n n C1 O5 NAG sing 298 n n C1 H1 NAG sing 299 n n C2 C3 NAG sing 300 n n C2 N2 NAG sing 301 n n C2 H2 NAG sing 302 n n C3 C4 NAG sing 303 n n C3 O3 NAG sing 304 n n C3 H3 NAG sing 305 n n C4 C5 NAG sing 306 n n C4 O4 NAG sing 307 n n C4 H4 NAG sing 308 n n C5 C6 NAG sing 309 n n C5 O5 NAG sing 310 n n C5 H5 NAG sing 311 n n C6 O6 NAG sing 312 n n C6 H61 NAG sing 313 n n C6 H62 NAG sing 314 n n C7 C8 NAG sing 315 n n C7 N2 NAG sing 316 n n C7 O7 NAG doub 317 n n C8 H81 NAG sing 318 n n C8 H82 NAG sing 319 n n C8 H83 NAG sing 320 n n N2 HN2 NAG sing 321 n n O1 HO1 NAG sing 322 n n O3 HO3 NAG sing 323 n n O4 HO4 NAG sing 324 n n O6 HO6 NAG sing 325 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 5K33 _atom_sites.fract_transf_matrix[1][1] 0.009206 _atom_sites.fract_transf_matrix[1][2] 0.005315 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010631 _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] 0.005736 _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 E 5 GOL A 1 506 5 GOL GOL . F 6 NAG C 1 705 587 NAG NAG . G 6 NAG C 1 706 588 NAG NAG . # 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 -18.192 18.098 -10.938 1 131.19 ? C1 NAG 705 C 1 HETATM 2 C C2 NAG . . . F 6 -18.521 18.462 -12.398 1 140.39 ? C2 NAG 705 C 1 HETATM 3 C C3 NAG . . . F 6 -19.99 18.868 -12.536 1 135.37 ? C3 NAG 705 C 1 HETATM 4 C C4 NAG . . . F 6 -20.904 17.807 -11.939 1 135.68 ? C4 NAG 705 C 1 HETATM 5 C C5 NAG . . . F 6 -20.499 17.529 -10.497 1 128.78 ? C5 NAG 705 C 1 HETATM 6 C C6 NAG . . . F 6 -21.304 16.42 -9.859 1 128.31 ? C6 NAG 705 C 1 HETATM 7 C C7 NAG . . . F 6 -16.608 19.335 -13.681 1 147.75 ? C7 NAG 705 C 1 HETATM 8 C C8 NAG . . . F 6 -15.836 20.562 -14.067 1 146.2 ? C8 NAG 705 C 1 HETATM 9 N N2 NAG . . . F 6 -17.656 19.533 -12.873 1 143.11 ? N2 NAG 705 C 1 HETATM 10 O O3 NAG . . . F 6 -20.302 19.048 -13.913 1 137.63 ? O3 NAG 705 C 1 HETATM 11 O O4 NAG . . . F 6 -22.255 18.254 -11.976 1 135.51 ? O4 NAG 705 C 1 HETATM 12 O O5 NAG . . . F 6 -19.126 17.115 -10.46 1 131.47 ? O5 NAG 705 C 1 HETATM 13 O O6 NAG . . . F 6 -22.626 16.84 -9.548 1 127.38 ? O6 NAG 705 C 1 HETATM 14 O O7 NAG . . . F 6 -16.295 18.217 -14.08 1 150.01 ? O7 NAG 705 C 1 HETATM 15 H H1 NAG . . . F 6 -18.255 18.899 -10.384 1 157.43 ? H1 NAG 705 C 1 HETATM 16 H H2 NAG . . . F 6 -18.371 17.673 -12.952 1 168.47 ? H2 NAG 705 C 1 HETATM 17 H H3 NAG . . . F 6 -20.132 19.711 -12.065 1 162.45 ? H3 NAG 705 C 1 HETATM 18 H H4 NAG . . . F 6 -20.823 16.985 -12.459 1 162.82 ? H4 NAG 705 C 1 HETATM 19 H H5 NAG . . . F 6 -20.603 18.345 -9.972 1 154.54 ? H5 NAG 705 C 1 HETATM 20 H H61 NAG . . . F 6 -20.859 16.136 -9.037 1 153.97 ? H61 NAG 705 C 1 HETATM 21 H H62 NAG . . . F 6 -21.347 15.663 -10.474 1 153.97 ? H62 NAG 705 C 1 HETATM 22 H H81 NAG . . . F 6 -15.484 20.991 -13.265 1 175.44 ? H81 NAG 705 C 1 HETATM 23 H H82 NAG . . . F 6 -15.098 20.311 -14.653 1 175.44 ? H82 NAG 705 C 1 HETATM 24 H H83 NAG . . . F 6 -16.426 21.183 -14.535 1 175.44 ? H83 NAG 705 C 1 HETATM 25 H HN2 NAG . . . F 6 -17.842 20.386 -12.609 1 171.73 ? HN2 NAG 705 C 1 HETATM 26 H HO3 NAG . . . F 6 -21.153 18.836 -14.054 1 165.15 ? HO3 NAG 705 C 1 HETATM 27 H HO4 NAG . . . F 6 -22.793 17.592 -11.729 1 162.62 ? HO4 NAG 705 C 1 HETATM 28 H HO6 NAG . . . F 6 -23.065 16.172 -9.16 1 152.86 ? HO6 NAG 705 C 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #