data_4YFL # _model_server_result.job_id ij8l5BnsTLytWEKjri58rQ _model_server_result.datetime_utc '2024-11-27 01:25:11' _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 4yfl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":502}' # _entry.id 4YFL # _exptl.entry_id 4YFL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 16 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.11 _cell.angle_gamma 90 _cell.entry_id 4YFL _cell.length_a 66.962 _cell.length_b 57.318 _cell.length_c 254.715 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YFL _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 ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_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,G,H,I,J,K,L 1 1 D,E,F,M,N,O,P,Q,R,S,T,U,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 ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N ? 4 R N N ? 4 S N N ? 4 T N N ? 4 U N N ? 4 V N N # 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 G CYS 54 1_555 A SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 76 G CYS 119 1_555 A SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf3 A SG CYS 102 G CYS 218 1_555 A SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf4 A SG CYS 112 G CYS 228 1_555 A SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 180 G CYS 296 1_555 A SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 A SG CYS 245 G CYS 378 1_555 A SG CYS 306 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 A SG CYS 252 G CYS 385 1_555 A SG CYS 279 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 A SG CYS 262 G CYS 395 1_555 A SG CYS 271 G CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf9 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 152 H CYS 152 1_555 B SG CYS 208 H CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf11 C SG CYS 22 L CYS 23 1_555 C SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 C SG CYS 138 L CYS 134 1_555 C SG CYS 197 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf13 D SG CYS 11 E CYS 54 1_555 D SG CYS 31 E CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf14 D SG CYS 76 E CYS 119 1_555 D SG CYS 89 E CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf15 D SG CYS 102 E CYS 218 1_555 D SG CYS 131 E CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf16 D SG CYS 112 E CYS 228 1_555 D SG CYS 123 E CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf17 D SG CYS 180 E CYS 296 1_555 D SG CYS 199 E CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf18 D SG CYS 245 E CYS 378 1_555 D SG CYS 306 E CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf19 D SG CYS 252 E CYS 385 1_555 D SG CYS 279 E CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf20 D SG CYS 262 E CYS 395 1_555 D SG CYS 271 E CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf21 E SG CYS 22 F CYS 22 1_555 E SG CYS 96 F CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf22 E SG CYS 152 F CYS 140 1_555 E SG CYS 208 F CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf23 F SG CYS 22 I CYS 23 1_555 F SG CYS 89 I CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf24 F SG CYS 138 I CYS 134 1_555 F SG CYS 197 I CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 125 G ASN 241 1_555 G C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 A ND2 ASN 146 G ASN 262 1_555 H C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 173 G ASN 289 1_555 I C1 NAG . G NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale4 A ND2 ASN 179 G ASN 295 1_555 J C1 NAG . G NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale5 A ND2 ASN 202 G ASN 334 1_555 K C1 NAG . G NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 A ND2 ASN 259 G ASN 392 1_555 L C1 NAG . G NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale7 B CA LYS 63 H LYS 63 1_555 C OG SER 156 L SER 152 2_656 ? ? ? ? ? ? ? ? ? ? ? ? 1.202 ? covale ? covale8 D ND2 ASN 118 E ASN 234 1_555 N C1 NAG . E NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 D ND2 ASN 125 E ASN 241 1_555 O C1 NAG . E NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale10 D ND2 ASN 160 E ASN 276 1_555 P C1 NAG . E NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale11 D ND2 ASN 173 E ASN 289 1_555 Q C1 NAG . E NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale12 D ND2 ASN 179 E ASN 295 1_555 R C1 NAG . E NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale13 D ND2 ASN 202 E ASN 334 1_555 S C1 NAG . E NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale14 D ND2 ASN 253 E ASN 386 1_555 T C1 NAG . E NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 D ND2 ASN 259 E ASN 392 1_555 U C1 NAG . E NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale16 D ND2 ASN 272 E ASN 411 1_555 V C1 NAG . E NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? # _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 4YFL _atom_sites.fract_transf_matrix[1][1] 0.014934 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000028 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017447 _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] 0.003926 _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 G 4 NAG G 1 501 741 NAG NAG . H 4 NAG G 1 502 762 NAG NAG . I 4 NAG G 1 503 789 NAG NAG . J 4 NAG G 1 504 795 NAG NAG . K 4 NAG G 1 505 834 NAG NAG . L 4 NAG G 1 506 892 NAG NAG . M 4 NAG E 1 501 588 NAG NAG . N 4 NAG E 1 502 734 NAG NAG . O 4 NAG E 1 503 741 NAG NAG . P 4 NAG E 1 504 776 NAG NAG . Q 4 NAG E 1 505 789 NAG NAG . R 4 NAG E 1 506 795 NAG NAG . S 4 NAG E 1 507 834 NAG NAG . T 4 NAG E 1 508 886 NAG NAG . U 4 NAG E 1 509 892 NAG NAG . V 4 NAG E 1 510 911 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 . . . N 4 -39.429 -22.096 52.817 1 94.14 ? C1 NAG 502 E 1 HETATM 2 C C2 NAG . . . N 4 -38.53 -20.981 52.258 1 103.99 ? C2 NAG 502 E 1 HETATM 3 C C3 NAG . . . N 4 -39.021 -20.524 50.882 1 106.65 ? C3 NAG 502 E 1 HETATM 4 C C4 NAG . . . N 4 -39.203 -21.714 49.949 1 115.54 ? C4 NAG 502 E 1 HETATM 5 C C5 NAG . . . N 4 -40.127 -22.731 50.601 1 135.57 ? C5 NAG 502 E 1 HETATM 6 C C6 NAG . . . N 4 -40.315 -23.989 49.778 1 187.88 ? C6 NAG 502 E 1 HETATM 7 C C7 NAG . . . N 4 -37.605 -18.829 53.022 1 139.88 ? C7 NAG 502 E 1 HETATM 8 C C8 NAG . . . N 4 -37.667 -17.752 54.064 1 105.84 ? C8 NAG 502 E 1 HETATM 9 N N2 NAG . . . N 4 -38.455 -19.852 53.177 1 133.47 ? N2 NAG 502 E 1 HETATM 10 O O3 NAG . . . N 4 -38.085 -19.614 50.316 1 103.89 ? O3 NAG 502 E 1 HETATM 11 O O4 NAG . . . N 4 -39.771 -21.296 48.712 1 131.91 ? O4 NAG 502 E 1 HETATM 12 O O5 NAG . . . N 4 -39.563 -23.136 51.855 1 108.98 ? O5 NAG 502 E 1 HETATM 13 O O6 NAG . . . N 4 -39.919 -23.803 48.425 1 222.74 ? O6 NAG 502 E 1 HETATM 14 O O7 NAG . . . N 4 -36.831 -18.77 52.074 1 198.77 ? O7 NAG 502 E 1 HETATM 15 H H1 NAG . . . N 4 -40.311 -21.728 53.019 1 112.97 ? H1 NAG 502 E 1 HETATM 16 H H2 NAG . . . N 4 -37.631 -21.345 52.147 1 124.79 ? H2 NAG 502 E 1 HETATM 17 H H3 NAG . . . N 4 -39.879 -20.071 50.987 1 127.98 ? H3 NAG 502 E 1 HETATM 18 H H4 NAG . . . N 4 -38.335 -22.128 49.782 1 138.65 ? H4 NAG 502 E 1 HETATM 19 H H5 NAG . . . N 4 -40.998 -22.319 50.758 1 162.68 ? H5 NAG 502 E 1 HETATM 20 H H61 NAG . . . N 4 -41.257 -24.245 49.801 1 225.46 ? H61 NAG 502 E 1 HETATM 21 H H62 NAG . . . N 4 -39.781 -24.706 50.169 1 225.46 ? H62 NAG 502 E 1 HETATM 22 H H81 NAG . . . N 4 -37.511 -18.142 54.945 1 127.01 ? H81 NAG 502 E 1 HETATM 23 H H82 NAG . . . N 4 -38.548 -17.332 54.046 1 127.01 ? H82 NAG 502 E 1 HETATM 24 H H83 NAG . . . N 4 -36.983 -17.081 53.879 1 127.01 ? H83 NAG 502 E 1 HETATM 25 H HN2 NAG . . . N 4 -39.012 -19.845 53.899 1 160.16 ? HN2 NAG 502 E 1 HETATM 26 H HO3 NAG . . . N 4 -38.266 -18.791 50.597 1 124.67 ? HO3 NAG 502 E 1 HETATM 27 H HO4 NAG . . . N 4 -39.292 -20.628 48.377 1 158.29 ? HO4 NAG 502 E 1 HETATM 28 H HO6 NAG . . . N 4 -40.577 -24.059 47.887 1 267.29 ? HO6 NAG 502 E 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #