data_5YLV # _model_server_result.job_id k0s2w59AKvyycEFdCxJjpQ _model_server_result.datetime_utc '2024-11-15 03:04:25' _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 5ylv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":303}' # _entry.id 5YLV # _exptl.entry_id 5YLV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method syn _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 120 _cell.entry_id 5YLV _cell.length_a 105.05 _cell.length_b 105.05 _cell.length_c 368.54 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLV _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 _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 ? 7 I N N ? 7 J N N ? 7 K 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 B SG CYS 130 B CYS 131 1_555 B SG CYS 151 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 B SG CYS 161 B CYS 162 1_555 B SG CYS 177 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 200 B CYS 201 1_555 B SG CYS 261 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A C SER 385 A SER 384 1_555 A N BFD 386 A BFD 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C BFD 386 A BFD 385 1_555 A N LYS 387 A LYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale3 B ND2 ASN 98 B ASN 99 1_555 I C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 B ND2 ASN 129 B ASN 130 1_555 J C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale5 B OE1 GLN 138 B GLN 139 1_555 B CG LYS 148 B LYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.129 ? covale ? covale6 B OE1 GLN 138 B GLN 139 1_555 B CD LYS 148 B LYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? covale ? covale7 B ND2 ASN 160 B ASN 161 1_555 K C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A O ASP 184 A ASP 183 1_555 H RB RB . A RB 1106 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc2 A OD2 ASP 186 A ASP 185 1_555 H RB RB . A RB 1106 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc3 A O VAL 342 A VAL 341 1_555 F RB RB . A RB 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc4 A OD2 BFD 386 A BFD 385 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc5 A O THR 388 A THR 387 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc6 A O SER 409 A SER 408 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc7 A OG SER 409 A SER 408 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc8 A O GLN 419 A GLN 418 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.166 ? metalc ? metalc9 A O THR 420 A THR 419 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.129 ? metalc ? metalc10 A OD1 ASP 727 A ASP 726 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc11 A O LYS 736 A LYS 735 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc12 A O ALA 738 A ALA 737 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc13 A OD1 ASP 757 A ASP 756 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? # _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 387 n n C1 O1 NAG sing 388 n n C1 O5 NAG sing 389 n n C1 H1 NAG sing 390 n n C2 C3 NAG sing 391 n n C2 N2 NAG sing 392 n n C2 H2 NAG sing 393 n n C3 C4 NAG sing 394 n n C3 O3 NAG sing 395 n n C3 H3 NAG sing 396 n n C4 C5 NAG sing 397 n n C4 O4 NAG sing 398 n n C4 H4 NAG sing 399 n n C5 C6 NAG sing 400 n n C5 O5 NAG sing 401 n n C5 H5 NAG sing 402 n n C6 O6 NAG sing 403 n n C6 H61 NAG sing 404 n n C6 H62 NAG sing 405 n n C7 C8 NAG sing 406 n n C7 N2 NAG sing 407 n n C7 O7 NAG doub 408 n n C8 H81 NAG sing 409 n n C8 H82 NAG sing 410 n n C8 H83 NAG sing 411 n n N2 HN2 NAG sing 412 n n O1 HO1 NAG sing 413 n n O3 HO3 NAG sing 414 n n O4 HO4 NAG sing 415 n n O6 HO6 NAG sing 416 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 5YLV _atom_sites.fract_transf_matrix[1][1] 0.009519 _atom_sites.fract_transf_matrix[1][2] 0.005496 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010992 _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] 0.002713 _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 C 3 8WX A 1 1101 1101 8WX 8WX . D 4 MG A 1 1102 1102 MG MG . E 5 CE1 A 1 1103 1103 CE1 CE1 . F 6 RB A 1 1104 1104 RB RB . G 6 RB A 1 1105 1105 RB RB . H 6 RB A 1 1106 1106 RB RB . I 7 NAG B 1 301 301 NAG NAG . J 7 NAG B 1 302 302 NAG NAG . K 7 NAG B 1 303 303 NAG NAG . L 8 PCW B 1 304 304 PCW PCW . M 5 CE1 B 1 305 305 CE1 CE1 . N 9 HOH A 1 1201 1201 HOH HOH . N 9 HOH A 2 1202 1202 HOH HOH . N 9 HOH A 3 1203 1203 HOH HOH . N 9 HOH A 4 1204 1204 HOH HOH . N 9 HOH A 5 1205 1205 HOH HOH . N 9 HOH A 6 1206 1206 HOH HOH . N 9 HOH A 7 1207 1207 HOH HOH . N 9 HOH A 8 1208 1208 HOH HOH . N 9 HOH A 9 1209 1209 HOH HOH . N 9 HOH A 10 1210 1210 HOH HOH . N 9 HOH A 11 1211 1211 HOH HOH . N 9 HOH A 12 1212 1212 HOH HOH . N 9 HOH A 13 1213 1213 HOH HOH . N 9 HOH A 14 1214 1214 HOH HOH . N 9 HOH A 15 1215 1215 HOH HOH . N 9 HOH A 16 1216 1216 HOH HOH . N 9 HOH A 17 1217 1217 HOH HOH . N 9 HOH A 18 1218 1218 HOH HOH . N 9 HOH A 19 1219 1219 HOH HOH . N 9 HOH A 20 1220 1220 HOH HOH . N 9 HOH A 21 1221 1221 HOH HOH . N 9 HOH A 22 1222 1222 HOH HOH . O 9 HOH B 1 401 401 HOH HOH . O 9 HOH B 2 402 402 HOH HOH . O 9 HOH B 3 403 403 HOH HOH . O 9 HOH B 4 404 404 HOH HOH . O 9 HOH B 5 405 405 HOH HOH . O 9 HOH B 6 406 406 HOH HOH . O 9 HOH B 7 407 407 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 . . . K 7 58.509 -16.388 -60.179 1 100.81 ? C1 NAG 303 B 1 HETATM 2 C C2 NAG . . . K 7 59.378 -17.605 -60.502 1 106.19 ? C2 NAG 303 B 1 HETATM 3 C C3 NAG . . . K 7 60.077 -17.396 -61.836 1 101.89 ? C3 NAG 303 B 1 HETATM 4 C C4 NAG . . . K 7 59.037 -17.168 -62.922 1 104.01 ? C4 NAG 303 B 1 HETATM 5 C C5 NAG . . . K 7 58.154 -15.974 -62.547 1 105.18 ? C5 NAG 303 B 1 HETATM 6 C C6 NAG . . . K 7 57.021 -15.739 -63.519 1 105.97 ? C6 NAG 303 B 1 HETATM 7 C C7 NAG . . . K 7 60.319 -18.985 -58.707 1 105.6 ? C7 NAG 303 B 1 HETATM 8 C C8 NAG . . . K 7 61.406 -19.115 -57.687 1 102.19 ? C8 NAG 303 B 1 HETATM 9 N N2 NAG . . . K 7 60.349 -17.877 -59.454 1 108.09 ? N2 NAG 303 B 1 HETATM 10 O O3 NAG . . . K 7 60.904 -18.511 -62.145 1 98.71 ? O3 NAG 303 B 1 HETATM 11 O O4 NAG . . . K 7 59.693 -16.934 -64.162 1 104.52 ? O4 NAG 303 B 1 HETATM 12 O O5 NAG . . . K 7 57.557 -16.173 -61.253 1 102.21 ? O5 NAG 303 B 1 HETATM 13 O O6 NAG . . . K 7 56.215 -14.637 -63.122 1 109.09 ? O6 NAG 303 B 1 HETATM 14 O O7 NAG . . . K 7 59.445 -19.84 -58.844 1 107.82 ? O7 NAG 303 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #