data_6YLA # _model_server_result.job_id jbEeoOtIG010yyNg08ia2Q _model_server_result.datetime_utc '2024-11-21 09:02:08' _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 6yla # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":904}' # _entry.id 6YLA # _exptl.entry_id 6YLA _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 3 _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 90 _cell.entry_id 6YLA _cell.length_a 163.124 _cell.length_b 163.124 _cell.length_c 189.076 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YLA _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' # 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,M,N,O,P,Q,R,S,T,U,V,MA,NA,OA 1 1 D,E,F,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,PA,QA,RA 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 L N N ? 6 M N N ? 6 Z 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 10 E CYS 336 1_555 A SG CYS 35 E CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 53 E CYS 379 1_555 A SG CYS 106 E CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 65 E CYS 391 1_555 A SG CYS 199 E CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 154 E CYS 480 1_555 A SG CYS 162 E CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 23 H CYS 22 1_555 B SG CYS 97 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 145 H CYS 144 1_555 B SG CYS 201 H CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 C SG CYS 23 L CYS 23 1_555 C SG CYS 94 L CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 C SG CYS 140 L CYS 140 1_555 C SG CYS 200 L CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 D SG CYS 10 A CYS 336 1_555 D SG CYS 35 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 D SG CYS 53 A CYS 379 1_555 D SG CYS 106 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 D SG CYS 65 A CYS 391 1_555 D SG CYS 199 A CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 D SG CYS 154 A CYS 480 1_555 D SG CYS 162 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 E SG CYS 23 B CYS 22 1_555 E SG CYS 97 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 E SG CYS 145 B CYS 144 1_555 E SG CYS 201 B CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 F SG CYS 23 C CYS 23 1_555 F SG CYS 94 C CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 F SG CYS 140 C CYS 140 1_555 F SG CYS 200 C CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 5 E ASN 331 1_555 L C1 NAG . E NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 17 E ASN 343 1_555 M C1 NAG . E NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 D ND2 ASN 17 A ASN 343 1_555 Z C1 NAG . A NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _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 291 n n C1 O1 NAG sing 292 n n C1 O5 NAG sing 293 n n C1 H1 NAG sing 294 n n C2 C3 NAG sing 295 n n C2 N2 NAG sing 296 n n C2 H2 NAG sing 297 n n C3 C4 NAG sing 298 n n C3 O3 NAG sing 299 n n C3 H3 NAG sing 300 n n C4 C5 NAG sing 301 n n C4 O4 NAG sing 302 n n C4 H4 NAG sing 303 n n C5 C6 NAG sing 304 n n C5 O5 NAG sing 305 n n C5 H5 NAG sing 306 n n C6 O6 NAG sing 307 n n C6 H61 NAG sing 308 n n C6 H62 NAG sing 309 n n C7 C8 NAG sing 310 n n C7 N2 NAG sing 311 n n C7 O7 NAG doub 312 n n C8 H81 NAG sing 313 n n C8 H82 NAG sing 314 n n C8 H83 NAG sing 315 n n N2 HN2 NAG sing 316 n n O1 HO1 NAG sing 317 n n O3 HO3 NAG sing 318 n n O4 HO4 NAG sing 319 n n O6 HO6 NAG sing 320 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 6YLA _atom_sites.fract_transf_matrix[1][1] 0.00613 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00613 _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] 0.005289 _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 DMS E 1 901 901 DMS DMS . H 4 DMS E 1 902 1001 DMS DMS . I 5 MLI E 1 903 1101 MLI MLI . J 4 DMS E 1 904 1201 DMS DMS . K 4 DMS E 1 905 1301 DMS DMS . L 6 NAG E 1 906 1401 NAG NAG . M 6 NAG E 1 907 1501 NAG NAG . N 5 MLI E 1 908 601 MLI MLI . O 5 MLI H 1 301 301 MLI MLI . P 4 DMS H 1 302 501 DMS DMS . Q 4 DMS H 1 303 701 DMS DMS . R 5 MLI H 1 304 801 MLI MLI . S 5 MLI H 1 305 901 MLI MLI . T 4 DMS L 1 1601 1601 DMS DMS . U 4 DMS L 1 1602 401 DMS DMS . V 7 1PE L 1 1603 301 1PE 1PE . W 4 DMS A 1 901 901 DMS DMS . X 8 PG0 A 1 902 1001 PG0 PG0 . Y 4 DMS A 1 903 1101 DMS DMS . Z 6 NAG A 1 904 1201 NAG NAG . AA 4 DMS A 1 905 1301 DMS DMS . BA 5 MLI B 1 301 301 MLI MLI . CA 5 MLI B 1 302 401 MLI MLI . DA 5 MLI B 1 303 501 MLI MLI . EA 5 MLI B 1 304 601 MLI MLI . FA 4 DMS B 1 305 401 DMS DMS . GA 7 1PE C 1 301 301 1PE 1PE . HA 4 DMS C 1 302 701 DMS DMS . IA 4 DMS C 1 303 801 DMS DMS . JA 5 MLI C 1 304 901 MLI MLI . KA 5 MLI C 1 305 1001 MLI MLI . LA 5 MLI C 1 306 1101 MLI MLI . MA 9 HOH E 1 1001 49 HOH HOH . MA 9 HOH E 2 1002 63 HOH HOH . MA 9 HOH E 3 1003 193 HOH HOH . MA 9 HOH E 4 1004 93 HOH HOH . MA 9 HOH E 5 1005 133 HOH HOH . MA 9 HOH E 6 1006 67 HOH HOH . NA 9 HOH H 1 401 59 HOH HOH . NA 9 HOH H 2 402 83 HOH HOH . NA 9 HOH H 3 403 65 HOH HOH . NA 9 HOH H 4 404 117 HOH HOH . NA 9 HOH H 5 405 120 HOH HOH . NA 9 HOH H 6 406 175 HOH HOH . NA 9 HOH H 7 407 148 HOH HOH . NA 9 HOH H 8 408 204 HOH HOH . NA 9 HOH H 9 409 205 HOH HOH . OA 9 HOH L 1 1701 77 HOH HOH . OA 9 HOH L 2 1702 149 HOH HOH . OA 9 HOH L 3 1703 110 HOH HOH . OA 9 HOH L 4 1704 112 HOH HOH . OA 9 HOH L 5 1705 103 HOH HOH . OA 9 HOH L 6 1706 163 HOH HOH . OA 9 HOH L 7 1707 166 HOH HOH . OA 9 HOH L 8 1708 98 HOH HOH . OA 9 HOH L 9 1709 16 HOH HOH . PA 9 HOH A 1 1001 203 HOH HOH . PA 9 HOH A 2 1002 45 HOH HOH . PA 9 HOH A 3 1003 168 HOH HOH . PA 9 HOH A 4 1004 207 HOH HOH . QA 9 HOH B 1 401 48 HOH HOH . QA 9 HOH B 2 402 186 HOH HOH . QA 9 HOH B 3 403 208 HOH HOH . QA 9 HOH B 4 404 108 HOH HOH . QA 9 HOH B 5 405 76 HOH HOH . QA 9 HOH B 6 406 206 HOH HOH . QA 9 HOH B 7 407 152 HOH HOH . QA 9 HOH B 8 408 146 HOH HOH . QA 9 HOH B 9 409 109 HOH HOH . QA 9 HOH B 10 410 104 HOH HOH . RA 9 HOH C 1 401 201 HOH HOH . RA 9 HOH C 2 402 56 HOH HOH . RA 9 HOH C 3 403 3 HOH HOH . RA 9 HOH C 4 404 47 HOH HOH . RA 9 HOH C 5 405 136 HOH HOH . RA 9 HOH C 6 406 92 HOH HOH . RA 9 HOH C 7 407 172 HOH HOH . RA 9 HOH C 8 408 95 HOH HOH . RA 9 HOH C 9 409 36 HOH HOH . RA 9 HOH C 10 410 147 HOH HOH . RA 9 HOH C 11 411 122 HOH HOH . RA 9 HOH C 12 412 142 HOH HOH . RA 9 HOH C 13 413 33 HOH HOH . RA 9 HOH C 14 414 29 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 . . . Z 6 1.059 27.189 71.771 1 86.79 ? C1 NAG 904 A 1 HETATM 2 C C2 NAG . . . Z 6 1.956 28.443 71.563 1 96.17 ? C2 NAG 904 A 1 HETATM 3 C C3 NAG . . . Z 6 2.331 28.612 70.079 1 100.03 ? C3 NAG 904 A 1 HETATM 4 C C4 NAG . . . Z 6 2.828 27.308 69.472 1 97.92 ? C4 NAG 904 A 1 HETATM 5 C C5 NAG . . . Z 6 1.784 26.231 69.705 1 92.01 ? C5 NAG 904 A 1 HETATM 6 C C6 NAG . . . Z 6 2.159 24.883 69.139 1 83.15 ? C6 NAG 904 A 1 HETATM 7 C C7 NAG . . . Z 6 1.86 30.675 72.632 1 109.71 ? C7 NAG 904 A 1 HETATM 8 C C8 NAG . . . Z 6 3.342 30.568 72.839 1 109.59 ? C8 NAG 904 A 1 HETATM 9 N N2 NAG . . . Z 6 1.264 29.633 72.036 1 101.42 ? N2 NAG 904 A 1 HETATM 10 O O3 NAG . . . Z 6 3.333 29.612 69.934 1 104.09 ? O3 NAG 904 A 1 HETATM 11 O O4 NAG . . . Z 6 3.044 27.47 68.075 1 95.84 ? O4 NAG 904 A 1 HETATM 12 O O5 NAG . . . Z 6 1.638 26.062 71.116 1 98.49 ? O5 NAG 904 A 1 HETATM 13 O O6 NAG . . . Z 6 1.005 24.071 68.967 1 72.06 ? O6 NAG 904 A 1 HETATM 14 O O7 NAG . . . Z 6 1.224 31.659 73 1 117.08 ? O7 NAG 904 A 1 # _model_server_stats.io_time_ms 153 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #