data_7LY3 # _model_server_result.job_id RipsOUA8nzZykYedJgUO8w _model_server_result.datetime_utc '2024-10-19 10:36:16' _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 7ly3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":1704}' # _entry.id 7LY3 # _exptl.entry_id 7LY3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 152.146 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Xylitol _entity.pdbx_number_of_molecules 2 _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 7LY3 _cell.length_a 66.444 _cell.length_b 125.457 _cell.length_c 365.946 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LY3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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,C,D,G,H,I,J,K,P,Q,R,S,Y 1 1 B,E,F,L,M,N,O,T,U,V,W,X,Z 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 ? 9 S N N ? 9 X N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 1 FUC NAG C1 O1 . O6 HO6 . sing 4 ? 5 2 1 FUC NAG C1 O1 . O6 HO6 . sing 5 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 6 4 3 MAN BMA C1 O1 . O6 HO6 . sing 8 ? 6 5 1 FUC NAG C1 O1 . O6 HO6 . 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 4 n G NAG 1 G 1 NAG A 1314 NAG 4 n G NAG 2 G 2 NAG A 1315 NAG 4 n G BMA 3 G 3 BMA A 1316 BMA 4 n G FUC 4 G 4 FUC A 1313 FUC 5 n H NAG 1 H 1 NAG A 1401 NAG 5 n H FUC 2 H 2 FUC A 1400 FUC 4 n I NAG 1 I 1 NAG A 1414 NAG 4 n I NAG 2 I 2 NAG A 1415 NAG 4 n I BMA 3 I 3 BMA A 1416 BMA 4 n I FUC 4 I 4 FUC A 1413 FUC 5 n J NAG 1 J 1 NAG A 1614 NAG 5 n J FUC 2 J 2 FUC A 1613 FUC 6 n K NAG 1 K 1 NAG A 1725 NAG 6 n K NAG 2 K 2 NAG A 1726 NAG 6 n K BMA 3 K 3 BMA A 1727 BMA 6 n K MAN 4 K 4 MAN A 1728 MAN 6 n K FUC 5 K 5 FUC A 1724 FUC 6 n L NAG 1 L 1 NAG B 1314 NAG 6 n L NAG 2 L 2 NAG B 1315 NAG 6 n L BMA 3 L 3 BMA B 1316 BMA 6 n L MAN 4 L 4 MAN B 1317 MAN 6 n L FUC 5 L 5 FUC B 1313 FUC 4 n M NAG 1 M 1 NAG B 1414 NAG 4 n M NAG 2 M 2 NAG B 1415 NAG 4 n M BMA 3 M 3 BMA B 1416 BMA 4 n M FUC 4 M 4 FUC B 1413 FUC 5 n N NAG 1 N 1 NAG B 1902 NAG 5 n N FUC 2 N 2 FUC B 1901 FUC 5 n O NAG 1 O 1 NAG B 2002 NAG 5 n O FUC 2 O 2 FUC B 2003 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 34 A CYS 15 1_555 A SG CYS 155 A CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 150 A CYS 131 1_555 A SG CYS 185 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 310 A CYS 291 1_555 A SG CYS 320 A CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 B SG CYS 34 B CYS 15 1_555 B SG CYS 155 B CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 150 B CYS 131 1_555 B SG CYS 185 B CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 B SG CYS 310 B CYS 291 1_555 B SG CYS 320 B CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 C SG CYS 22 D CYS 22 1_555 C SG CYS 96 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf8 C SG CYS 146 D CYS 146 1_555 C SG CYS 202 D CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf9 D SG CYS 22 C CYS 22 1_555 D SG CYS 87 C CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf10 D SG CYS 136 C CYS 136 1_555 D SG CYS 195 C CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf11 E SG CYS 22 E CYS 22 1_555 E SG CYS 87 E CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 E SG CYS 136 E CYS 136 1_555 E SG CYS 195 E CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf13 F SG CYS 22 F CYS 22 1_555 F SG CYS 96 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf14 F SG CYS 146 F CYS 146 1_555 F SG CYS 202 F CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 36 A ASN 17 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 80 A ASN 61 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 A ND2 ASN 141 A ASN 122 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 168 A ASN 149 1_555 Q C1 NAG . A NAG 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 A ND2 ASN 184 A ASN 165 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale6 A ND2 ASN 253 A ASN 234 1_555 P C1 NAG . A NAG 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 A ND2 ASN 301 A ASN 282 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 B ND2 ASN 36 B ASN 17 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale9 B ND2 ASN 80 B ASN 61 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale10 B ND2 ASN 141 B ASN 122 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale11 B ND2 ASN 168 B ASN 149 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale12 B ND2 ASN 184 B ASN 165 1_555 T C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale13 B ND2 ASN 253 B ASN 234 1_555 U C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale14 B ND2 ASN 301 B ASN 282 1_555 V C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale15 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale16 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale17 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale18 H O6 NAG . H NAG 1 1_555 H C1 FUC . H FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale20 I O6 NAG . I NAG 1 1_555 I C1 FUC . I FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale21 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale22 J O6 NAG . J NAG 1 1_555 J C1 FUC . J FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale23 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale24 K O6 NAG . K NAG 1 1_555 K C1 FUC . K FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale25 K O4 NAG . K NAG 2 1_555 K C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale26 K O6 BMA . K BMA 3 1_555 K C1 MAN . K MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale27 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale28 L O6 NAG . L NAG 1 1_555 L C1 FUC . L FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale29 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale30 L O6 BMA . L BMA 3 1_555 L C1 MAN . L MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale31 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale32 M O6 NAG . M NAG 1 1_555 M C1 FUC . M FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale33 M O4 NAG . M NAG 2 1_555 M C1 BMA . M BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale34 N O6 NAG . N NAG 1 1_555 N C1 FUC . N FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale35 O O6 NAG . O NAG 1 1_555 O C1 FUC . O FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? # _chem_comp.formula 'C5 H12 O5' _chem_comp.formula_weight 152.146 _chem_comp.id XYL _chem_comp.mon_nstd_flag . _chem_comp.name Xylitol _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms D-Xylitol # 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 XYL sing 479 n n C1 O1 XYL sing 480 n n C1 H11 XYL sing 481 n n C1 H12 XYL sing 482 n n C2 C3 XYL sing 483 n n C2 O2 XYL sing 484 n n C2 H2 XYL sing 485 n n C3 C4 XYL sing 486 n n C3 O3 XYL sing 487 n n C3 H3 XYL sing 488 n n C4 C5 XYL sing 489 n n C4 O4 XYL sing 490 n n C4 H4 XYL sing 491 n n C5 O5 XYL sing 492 n n C5 H51 XYL sing 493 n n C5 H52 XYL sing 494 n n O1 HO1 XYL sing 495 n n O2 HO2 XYL sing 496 n n O3 HO3 XYL sing 497 n n O4 HO4 XYL sing 498 n n O5 HO5 XYL sing 499 n n # _atom_sites.entry_id 7LY3 _atom_sites.fract_transf_matrix[1][1] 0.01505 _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] 0.007971 _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] 0.002733 _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 P 7 NAG A 1 1701 1701 NAG NAG . Q 7 NAG A 1 1702 1902 NAG NAG . R 8 UNX A 1 1703 1 UNX CL . S 9 XYL A 1 1704 2002 XYL XYL . T 7 NAG B 1 401 1614 NAG NAG . U 7 NAG B 1 402 1701 NAG NAG . V 7 NAG B 1 403 1725 NAG NAG . W 8 UNX B 1 404 2 UNX CL . X 9 XYL B 1 405 2001 XYL XYL . Y 10 SO4 D 1 301 10 SO4 SO4 . Z 10 SO4 F 1 301 6 SO4 SO4 . # 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 XYL . . . S 9 8.195 5.37 90.183 1 105.29 ? C1 XYL 1704 A 1 HETATM 2 C C2 XYL . . . S 9 9.571 5.665 89.592 1 123.79 ? C2 XYL 1704 A 1 HETATM 3 C C3 XYL . . . S 9 10.701 5.482 90.593 1 142.29 ? C3 XYL 1704 A 1 HETATM 4 C C4 XYL . . . S 9 10.854 4.058 91.073 1 140.83 ? C4 XYL 1704 A 1 HETATM 5 C C5 XYL . . . S 9 11.373 3.101 89.999 1 129.17 ? C5 XYL 1704 A 1 HETATM 6 O O1 XYL . . . S 9 7.208 5.601 89.209 1 108.16 ? O1 XYL 1704 A 1 HETATM 7 O O2 XYL . . . S 9 9.763 4.82 88.488 1 108.13 ? O2 XYL 1704 A 1 HETATM 8 O O3 XYL . . . S 9 10.414 6.31 91.703 1 127.77 ? O3 XYL 1704 A 1 HETATM 9 O O4 XYL . . . S 9 11.765 4.032 92.153 1 114.4 ? O4 XYL 1704 A 1 HETATM 10 O O5 XYL . . . S 9 12.545 3.548 89.384 1 111.07 ? O5 XYL 1704 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #