data_5I9Q # _model_server_result.job_id NMMomyXGvxTjDhCpgDEvJA _model_server_result.datetime_utc '2024-12-31 11:40:23' _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 5i9q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":603}' # _entry.id 5I9Q # _exptl.entry_id 5I9Q _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 10 _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 5I9Q _cell.length_a 122.85 _cell.length_b 122.85 _cell.length_c 264.96 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5I9Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 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 PISA trimeric 3 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,C,D,G,I,J,K,L,M,N,O,U 1 1 B,E,F,H,P,Q,R,S,T,V 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 I N N ? 6 J N N ? 6 K N N ? 6 L N N ? 6 M N N ? 6 P N N ? 6 Q N N ? 6 R N N ? 6 U N N ? 6 V N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 4 6 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 8 ? 5 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 4 n G NAG 1 D 1 NAG A 608 NAG 4 n G NAG 2 D 2 NAG A 609 NAG 4 n G BMA 3 D 3 BMA A 610 BMA 4 n G MAN 4 D 4 MAN A 611 MAN 4 n G MAN 5 D 5 MAN A 612 MAN 4 n G MAN 6 D 6 MAN A 613 MAN 5 n H NAG 1 E 1 NAG G 606 NAG 5 n H NAG 2 E 2 NAG G 607 NAG 5 n H BMA 3 E 3 BMA G 608 BMA 5 n H MAN 4 E 4 MAN G 609 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 11 A CYS 54 1_555 A SG CYS 31 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 22 A CYS 65 1_555 A SG CYS 72 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 76 A CYS 119 1_555 A SG CYS 89 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 102 A CYS 218 1_555 A SG CYS 131 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 A SG CYS 180 A CYS 296 1_555 A SG CYS 199 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 245 A CYS 377 1_555 A SG CYS 298 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 A SG CYS 252 A CYS 384 1_555 A SG CYS 271 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 B SG CYS 11 G CYS 54 1_555 B SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 B SG CYS 22 G CYS 65 1_555 B SG CYS 72 G CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 B SG CYS 76 G CYS 119 1_555 B SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 B SG CYS 102 G CYS 218 1_555 B SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 B SG CYS 112 G CYS 228 1_555 B SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 B SG CYS 180 G CYS 296 1_555 B SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf14 B SG CYS 245 G CYS 377 1_555 B SG CYS 298 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf15 B SG CYS 252 G CYS 384 1_555 B SG CYS 271 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf16 C SG CYS 22 B CYS 22 1_555 C SG CYS 96 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf17 C SG CYS 146 B CYS 140 1_555 C SG CYS 202 B CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf18 D SG CYS 23 C CYS 23 1_555 D SG CYS 85 C CYS 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? disulf ? disulf19 D SG CYS 127 C CYS 127 1_555 D SG CYS 187 C CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf20 E SG CYS 22 H CYS 22 1_555 E SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 E SG CYS 146 H CYS 140 1_555 E SG CYS 202 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf22 F SG CYS 23 L CYS 23 1_555 F SG CYS 85 L CYS 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf23 F SG CYS 127 L CYS 127 1_555 F SG CYS 187 L CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A ND2 ASN 114 A ASN 230 1_555 I C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 125 A ASN 241 1_555 J C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 A ND2 ASN 146 A ASN 262 1_555 G C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.566 ? covale ? covale4 A ND2 ASN 205 A ASN 337 1_555 K C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 A ND2 ASN 253 A ASN 385 1_555 L C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale6 A ND2 ASN 264 A ASN 396 1_555 M C1 NAG . A NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 B ND2 ASN 114 G ASN 230 1_555 Q C1 NAG . G NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 B ND2 ASN 125 G ASN 241 1_555 R C1 NAG . G NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 B ND2 ASN 146 G ASN 262 1_555 H C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale10 B ND2 ASN 253 G ASN 385 1_555 P C1 NAG . G NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 C CA GLY 145 B GLY 139 1_555 C CG1 VAL 187 B VAL 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.633 ? covale ? covale12 D ND2 ASN 69 C ASN 69 1_555 U C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale13 F ND2 ASN 69 L ASN 69 1_555 V C1 NAG . L NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale14 G O4 NAG . D NAG 1 1_555 G C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale15 G O4 NAG . D NAG 2 1_555 G C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale16 G O3 BMA . D BMA 3 1_555 G C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale17 G O6 BMA . D BMA 3 1_555 G C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale18 G O2 MAN . D MAN 4 1_555 G C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale19 H O4 NAG . E NAG 1 1_555 H C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale20 H O4 NAG . E NAG 2 1_555 H C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale21 H O3 BMA . E BMA 3 1_555 H C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? # _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 292 n n C1 O1 NAG sing 293 n n C1 O5 NAG sing 294 n n C1 H1 NAG sing 295 n n C2 C3 NAG sing 296 n n C2 N2 NAG sing 297 n n C2 H2 NAG sing 298 n n C3 C4 NAG sing 299 n n C3 O3 NAG sing 300 n n C3 H3 NAG sing 301 n n C4 C5 NAG sing 302 n n C4 O4 NAG sing 303 n n C4 H4 NAG sing 304 n n C5 C6 NAG sing 305 n n C5 O5 NAG sing 306 n n C5 H5 NAG sing 307 n n C6 O6 NAG sing 308 n n C6 H61 NAG sing 309 n n C6 H62 NAG sing 310 n n C7 C8 NAG sing 311 n n C7 N2 NAG sing 312 n n C7 O7 NAG doub 313 n n C8 H81 NAG sing 314 n n C8 H82 NAG sing 315 n n C8 H83 NAG sing 316 n n N2 HN2 NAG sing 317 n n O1 HO1 NAG sing 318 n n O3 HO3 NAG sing 319 n n O4 HO4 NAG sing 320 n n O6 HO6 NAG sing 321 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 5I9Q _atom_sites.fract_transf_matrix[1][1] 0.00814 _atom_sites.fract_transf_matrix[1][2] 0.0047 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009399 _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] 0.003774 _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 I 6 NAG A 1 601 601 NAG NAG . J 6 NAG A 1 602 602 NAG NAG . K 6 NAG A 1 603 603 NAG NAG . L 6 NAG A 1 604 604 NAG NAG . M 6 NAG A 1 605 605 NAG NAG . N 7 EDO A 1 606 606 EDO EDO . O 7 EDO A 1 607 607 EDO EDO . P 6 NAG G 1 601 601 NAG NAG . Q 6 NAG G 1 602 602 NAG NAG . R 6 NAG G 1 603 603 NAG NAG . S 8 PGE G 1 604 604 PGE PGE . T 7 EDO G 1 605 605 EDO EDO . U 6 NAG C 1 301 301 NAG NAG . V 6 NAG L 1 301 301 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 . . . R 6 23.422 -17.327 -19.846 0.88 103.78 ? C1 NAG 603 G 1 HETATM 2 C C2 NAG . . . R 6 23.155 -17.809 -18.418 0.88 106.56 ? C2 NAG 603 G 1 HETATM 3 C C3 NAG . . . R 6 22.464 -16.717 -17.608 0.88 104.46 ? C3 NAG 603 G 1 HETATM 4 C C4 NAG . . . R 6 23.265 -15.424 -17.668 0.88 104.71 ? C4 NAG 603 G 1 HETATM 5 C C5 NAG . . . R 6 23.515 -15.029 -19.12 0.88 104.98 ? C5 NAG 603 G 1 HETATM 6 C C6 NAG . . . R 6 24.399 -13.811 -19.256 0.88 107.85 ? C6 NAG 603 G 1 HETATM 7 C C7 NAG . . . R 6 22.883 -20.243 -18.617 0.88 96.6 ? C7 NAG 603 G 1 HETATM 8 C C8 NAG . . . R 6 21.917 -21.388 -18.583 0.88 81.17 ? C8 NAG 603 G 1 HETATM 9 N N2 NAG . . . R 6 22.361 -19.028 -18.417 0.88 105.29 ? N2 NAG 603 G 1 HETATM 10 O O3 NAG . . . R 6 22.336 -17.146 -16.257 0.88 102.47 ? O3 NAG 603 G 1 HETATM 11 O O4 NAG . . . R 6 22.556 -14.38 -17.01 0.88 103.89 ? O4 NAG 603 G 1 HETATM 12 O O5 NAG . . . R 6 24.175 -16.101 -19.81 0.88 103.26 ? O5 NAG 603 G 1 HETATM 13 O O6 NAG . . . R 6 24.27 -13.214 -20.539 0.88 108.64 ? O6 NAG 603 G 1 HETATM 14 O O7 NAG . . . R 6 24.082 -20.41 -18.825 0.88 100.69 ? O7 NAG 603 G 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #