data_6RPJ # _model_server_result.job_id ABG4EALjN4AAqQQaUNVsHA _model_server_result.datetime_utc '2024-12-28 12:16:34' _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 6rpj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":202}' # _entry.id 6RPJ # _exptl.entry_id 6RPJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method nat _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 100.05 _cell.angle_gamma 90 _cell.entry_id 6RPJ _cell.length_a 309.977 _cell.length_b 75.708 _cell.length_c 83.047 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RPJ _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 tetrameric 4 software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression G,H,K,P,Q,S 1 1 A,B,I 1 2 C,D,E,F,J,L,M,N,O,R 2 1 # 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' 1_544 x,y-1,z-1 1 0 0 0 1 0 0 0 1 14.492326 -75.708 -81.772714 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 L N N ? 4 M N N ? 4 N N N ? 4 P 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 FUC _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 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _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 I NAG 1 I 1 NAG I 4 NAG 3 n I FUC 2 I 2 FUC K 3 FUC 3 n J NAG 1 J 1 NAG I 126 NAG 3 n J FUC 2 J 2 FUC K 1 FUC 3 n K NAG 1 K 1 NAG I 1 NAG 3 n K FUC 2 K 2 FUC K 2 FUC # 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 22 A CYS 23 1_555 A SG CYS 93 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 49 A CYS 50 1_555 A SG CYS 67 A CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 B SG CYS 22 B CYS 22 1_555 B SG CYS 96 B CYS 96 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 B SG CYS 22 B CYS 22 1_555 B SG CYS 96 B CYS 96 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 33 B CYS 33 1_555 B SG CYS 106 B CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 C SG CYS 22 C CYS 23 1_555 C SG CYS 93 C CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 C SG CYS 49 C CYS 50 1_555 C SG CYS 67 C CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 D SG CYS 22 D CYS 22 1_555 D SG CYS 96 D CYS 96 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 D SG CYS 22 D CYS 22 1_555 D SG CYS 96 D CYS 96 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 D SG CYS 33 D CYS 33 1_555 D SG CYS 106 D CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf11 E SG CYS 22 E CYS 23 1_555 E SG CYS 93 E CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 E SG CYS 49 E CYS 50 1_555 E SG CYS 67 E CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf13 F SG CYS 22 F CYS 22 1_555 F SG CYS 96 F CYS 96 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.038 ? disulf ? disulf14 F SG CYS 22 F CYS 22 1_555 F SG CYS 96 F CYS 96 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 F SG CYS 33 F CYS 33 1_555 F SG CYS 106 F CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf16 G SG CYS 22 G CYS 23 1_555 G SG CYS 93 G CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf17 G SG CYS 49 G CYS 50 1_555 G SG CYS 67 G CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf18 H SG CYS 22 H CYS 22 1_555 H SG CYS 96 H CYS 96 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.038 ? disulf ? disulf19 H SG CYS 22 H CYS 22 1_555 H SG CYS 96 H CYS 96 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.027 ? disulf ? disulf20 H SG CYS 33 H CYS 33 1_555 H SG CYS 106 H CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 77 A ASN 78 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 C ND2 ASN 77 C ASN 78 1_555 L C1 NAG . C NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 C ND2 ASN 109 C ASN 110 1_555 M C1 NAG . C NAG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 E ND2 ASN 77 E ASN 78 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 E ND2 ASN 109 E ASN 110 1_555 N C1 NAG . E NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 G ND2 ASN 77 G ASN 78 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 G ND2 ASN 109 G ASN 110 1_555 P C1 NAG . G NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 I O6 NAG . I NAG 1 1_555 I C1 FUC . I FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 J O6 NAG . J NAG 1 1_555 J C1 FUC . J FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 K O6 NAG . K NAG 1 1_555 K C1 FUC . K FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 E OE2 GLU 47 E GLU 48 1_555 O NA NA . E NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.023 ? metalc ? metalc2 G OE2 GLU 47 G GLU 48 1_555 Q NA NA . G NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? # _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 260 n n C1 O1 NAG sing 261 n n C1 O5 NAG sing 262 n n C1 H1 NAG sing 263 n n C2 C3 NAG sing 264 n n C2 N2 NAG sing 265 n n C2 H2 NAG sing 266 n n C3 C4 NAG sing 267 n n C3 O3 NAG sing 268 n n C3 H3 NAG sing 269 n n C4 C5 NAG sing 270 n n C4 O4 NAG sing 271 n n C4 H4 NAG sing 272 n n C5 C6 NAG sing 273 n n C5 O5 NAG sing 274 n n C5 H5 NAG sing 275 n n C6 O6 NAG sing 276 n n C6 H61 NAG sing 277 n n C6 H62 NAG sing 278 n n C7 C8 NAG sing 279 n n C7 N2 NAG sing 280 n n C7 O7 NAG doub 281 n n C8 H81 NAG sing 282 n n C8 H82 NAG sing 283 n n C8 H83 NAG sing 284 n n N2 HN2 NAG sing 285 n n O1 HO1 NAG sing 286 n n O3 HO3 NAG sing 287 n n O4 HO4 NAG sing 288 n n O6 HO6 NAG sing 289 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 6RPJ _atom_sites.fract_transf_matrix[1][1] 0.003226 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000572 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013209 _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] 0.012229 _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 L 4 NAG C 1 201 5 NAG NAG . M 4 NAG C 1 202 6 NAG NAG . N 4 NAG E 1 201 127 NAG NAG . O 5 NA E 1 202 2 NA NA . P 4 NAG G 1 201 128 NAG NAG . Q 5 NA G 1 202 1 NA NA . R 6 HOH D 1 201 1 HOH HOH . S 6 HOH H 1 201 4 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 . . . M 4 30.798 25.97 64.317 1 98.76 ? C1 NAG 202 C 1 HETATM 2 C C2 NAG . . . M 4 31.747 27.167 64.278 1 101.72 ? C2 NAG 202 C 1 HETATM 3 C C3 NAG . . . M 4 33.049 26.828 65.002 1 102.46 ? C3 NAG 202 C 1 HETATM 4 C C4 NAG . . . M 4 32.813 26.172 66.364 1 103.03 ? C4 NAG 202 C 1 HETATM 5 C C5 NAG . . . M 4 31.74 25.087 66.302 1 103.05 ? C5 NAG 202 C 1 HETATM 6 C C6 NAG . . . M 4 31.387 24.555 67.69 1 103.41 ? C6 NAG 202 C 1 HETATM 7 C C7 NAG . . . M 4 31.645 28.686 62.339 1 105.56 ? C7 NAG 202 C 1 HETATM 8 C C8 NAG . . . M 4 32.088 28.882 60.918 1 106.21 ? C8 NAG 202 C 1 HETATM 9 N N2 NAG . . . M 4 32.056 27.548 62.908 1 104.01 ? N2 NAG 202 C 1 HETATM 10 O O3 NAG . . . M 4 33.818 28.023 65.179 1 102.2 ? O3 NAG 202 C 1 HETATM 11 O O4 NAG . . . M 4 34.041 25.594 66.824 1 103.12 ? O4 NAG 202 C 1 HETATM 12 O O5 NAG . . . M 4 30.565 25.609 65.678 1 101.2 ? O5 NAG 202 C 1 HETATM 13 O O6 NAG . . . M 4 31.606 23.14 67.742 1 103.89 ? O6 NAG 202 C 1 HETATM 14 O O7 NAG . . . M 4 30.961 29.519 62.913 1 105.8 ? O7 NAG 202 C 1 # _model_server_stats.io_time_ms 123 _model_server_stats.parse_time_ms 62 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 1283 _model_server_stats.encode_time_ms 24 _model_server_stats.element_count 14 #