data_4NM8 # _model_server_result.job_id cb4yRmsI-HZecp3GXV4mSw _model_server_result.datetime_utc '2024-11-16 17:28:04' _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 4nm8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":501}' # _entry.id 4NM8 # _exptl.entry_id 4NM8 _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 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 133.46 _cell.angle_gamma 90 _cell.entry_id 4NM8 _cell.length_a 241.491 _cell.length_b 142.355 _cell.length_c 170.725 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NM8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 S N N ? 6 T N N ? 6 U N N ? 6 V N N ? 6 W N N ? 6 X N N ? 6 Y N N ? 6 Z 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 M NAG 1 G 1 NAG A 501 NAG 5 n M NAG 2 G 2 NAG A 502 NAG 5 n N NAG 1 K 1 NAG A 701 NAG 5 n N NAG 2 K 2 NAG A 702 NAG 5 n O NAG 1 O 1 NAG A 801 NAG 5 n O NAG 2 O 2 NAG A 802 NAG 5 n P NAG 1 P 1 NAG C 601 NAG 5 n P NAG 2 P 2 NAG C 602 NAG 5 n Q NAG 1 Q 1 NAG C 801 NAG 5 n Q NAG 2 Q 2 NAG C 802 NAG 5 n R NAG 1 R 1 NAG E 801 NAG 5 n R NAG 2 R 2 NAG E 802 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 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 271 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 133 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 A SG CYS 275 A CYS 281 1_555 A SG CYS 299 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf7 C SG CYS 8 C CYS 14 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 46 C CYS 52 1_555 C SG CYS 271 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf9 C SG CYS 58 C CYS 64 1_555 C SG CYS 70 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf10 C SG CYS 91 C CYS 97 1_555 C SG CYS 133 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf11 C SG CYS 275 C CYS 281 1_555 C SG CYS 299 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf13 E SG CYS 8 E CYS 14 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf14 E SG CYS 46 E CYS 52 1_555 E SG CYS 271 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf15 E SG CYS 58 E CYS 64 1_555 E SG CYS 70 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf16 E SG CYS 91 E CYS 97 1_555 E SG CYS 133 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 E SG CYS 275 E CYS 281 1_555 E SG CYS 299 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf19 G SG CYS 23 L CYS 23 1_555 G SG CYS 94 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf20 G SG CYS 140 L CYS 134 1_555 G SG CYS 200 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf21 H SG CYS 22 H CYS 22 1_555 H SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf22 H SG CYS 148 H CYS 140 1_555 H SG CYS 204 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf23 I SG CYS 23 M CYS 23 1_555 I SG CYS 94 M CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf24 I SG CYS 140 M CYS 134 1_555 I SG CYS 200 M CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf25 J SG CYS 22 I CYS 22 1_555 J SG CYS 96 I CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf26 J SG CYS 148 I CYS 140 1_555 J SG CYS 204 I CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf27 K SG CYS 23 N CYS 23 1_555 K SG CYS 94 N CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf28 K SG CYS 140 N CYS 134 1_555 K SG CYS 200 N CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf29 L SG CYS 22 J CYS 22 1_555 L SG CYS 96 J CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf30 L SG CYS 148 J CYS 140 1_555 L SG CYS 204 J CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 32 A ASN 38 1_555 M C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 159 A ASN 165 1_555 N C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 279 A ASN 285 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 B ND2 ASN 154 B ASN 154 1_555 S C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 C ND2 ASN 32 C ASN 38 1_555 T C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 C ND2 ASN 75 C ASN 81 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 C ND2 ASN 159 C ASN 165 1_555 U C1 NAG . C NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale8 C ND2 ASN 279 C ASN 285 1_555 Q C1 NAG . Q NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 D ND2 ASN 154 D ASN 154 1_555 V C1 NAG . D NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 E ND2 ASN 32 E ASN 38 1_555 W C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale11 E ND2 ASN 75 E ASN 81 1_555 X C1 NAG . E NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 E ND2 ASN 159 E ASN 165 1_555 Y C1 NAG . E NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale13 E ND2 ASN 279 E ASN 285 1_555 R C1 NAG . R NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale14 F ND2 ASN 154 F ASN 154 1_555 Z C1 NAG . F NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale15 M O4 NAG . G NAG 1 1_555 M C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale16 N O4 NAG . K NAG 1 1_555 N C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale17 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale18 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale19 Q O4 NAG . Q NAG 1 1_555 Q C1 NAG . Q NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale20 R O4 NAG . R NAG 1 1_555 R C1 NAG . R NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 4NM8 _atom_sites.fract_transf_matrix[1][1] 0.004141 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003924 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007025 _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] 0.00807 _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 S 6 NAG B 1 201 201 NAG NAG . T 6 NAG C 1 501 501 NAG NAG . U 6 NAG C 1 504 701 NAG NAG . V 6 NAG D 1 201 201 NAG NAG . W 6 NAG E 1 501 501 NAG NAG . X 6 NAG E 1 502 601 NAG NAG . Y 6 NAG E 1 503 701 NAG NAG . Z 6 NAG F 1 201 201 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 . . . T 6 -13.487 -0.432 61.693 1 86.53 ? C1 NAG 501 C 1 HETATM 2 C C2 NAG . . . T 6 -14.18 -1.502 62.534 1 93.22 ? C2 NAG 501 C 1 HETATM 3 C C3 NAG . . . T 6 -13.298 -2.708 62.833 1 97.1 ? C3 NAG 501 C 1 HETATM 4 C C4 NAG . . . T 6 -12.551 -3.171 61.588 1 97.46 ? C4 NAG 501 C 1 HETATM 5 C C5 NAG . . . T 6 -11.83 -1.989 60.954 1 88.87 ? C5 NAG 501 C 1 HETATM 6 C C6 NAG . . . T 6 -11.064 -2.422 59.709 1 92.29 ? C6 NAG 501 C 1 HETATM 7 C C7 NAG . . . T 6 -15.903 -1.023 64.146 1 96.41 ? C7 NAG 501 C 1 HETATM 8 C C8 NAG . . . T 6 -16.213 -0.743 65.588 1 94.66 ? C8 NAG 501 C 1 HETATM 9 N N2 NAG . . . T 6 -14.627 -0.938 63.79 1 96.41 ? N2 NAG 501 C 1 HETATM 10 O O3 NAG . . . T 6 -14.118 -3.747 63.322 1 94.23 ? O3 NAG 501 C 1 HETATM 11 O O4 NAG . . . T 6 -11.626 -4.191 61.905 1 98.45 ? O4 NAG 501 C 1 HETATM 12 O O5 NAG . . . T 6 -12.769 -0.99 60.608 1 81.72 ? O5 NAG 501 C 1 HETATM 13 O O6 NAG . . . T 6 -11.946 -3.051 58.806 1 88.85 ? O6 NAG 501 C 1 HETATM 14 O O7 NAG . . . T 6 -16.792 -1.317 63.345 1 91.05 ? O7 NAG 501 C 1 # _model_server_stats.io_time_ms 99 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #