data_4XUQ # _model_server_result.job_id YfG7Lw0e848jCfs_OrTvFw _model_server_result.datetime_utc '2024-11-15 11:33:18' _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 4xuq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 4XUQ # _exptl.entry_id 4XUQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description beta-D-xylopyranose _entity.pdbx_number_of_molecules 5 _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 4XUQ _cell.length_a 92.455 _cell.length_b 92.455 _cell.length_c 48.425 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XUQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,M 1 1 B,G,H,I,N 2 1 C,J,K,L,O 3 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 ? 3 E N N ? 3 G N N ? 3 H N N ? 3 J N N ? 3 K N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 XYP _pdbx_entity_branch_link.comp_id_2 XYP _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 2 n D XYP 1 D 1 XYP A 1003 XYP 2 n D XYP 2 D 2 XYP A 1002 XYP # 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 covale ? covale1 D O4 XYP . D XYP 1 1_555 D C1 XYP . D XYP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? metalc ? metalc1 A O ASP 19 A ASP 177 1_555 F CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc2 A OE2 GLU 21 A GLU 179 1_555 F CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc3 A OG SER 46 A SER 204 1_555 F CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc4 A O ARG 48 A ARG 206 1_555 F CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc5 A OD1 ASP 167 A ASP 325 1_555 F CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc6 A OD2 ASP 167 A ASP 325 1_555 F CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc7 F CA CA . A CA 1004 1_555 M O HOH . A HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc8 B O ASP 19 B ASP 177 1_555 I CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc9 B OE2 GLU 21 B GLU 179 1_555 I CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc10 B OG SER 46 B SER 204 1_555 I CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc11 B O ARG 48 B ARG 206 1_555 I CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc12 B OD1 ASP 167 B ASP 325 1_555 I CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc13 B OD2 ASP 167 B ASP 325 1_555 I CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc14 I CA CA . B CA 403 1_555 N O HOH . B HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc15 C O ASP 19 C ASP 177 1_555 L CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc16 C OE2 GLU 21 C GLU 179 1_555 L CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc17 C OG SER 46 C SER 204 1_555 L CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc18 C O ARG 48 C ARG 206 1_555 L CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc19 C OD1 ASP 167 C ASP 325 1_555 L CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc20 C OD2 ASP 167 C ASP 325 1_555 L CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc21 L CA CA . C CA 403 1_555 O O HOH . C HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? # _chem_comp.formula 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id XYP _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-xylopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-xylose;D-xylose;xylose # 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 O1 C1 XYP sing 363 n n O1 HO1 XYP sing 364 n n C1 C2 XYP sing 365 n n C1 O5 XYP sing 366 n n C1 H1 XYP sing 367 n n C2 C3 XYP sing 368 n n C2 O2 XYP sing 369 n n C2 H2 XYP sing 370 n n C3 C4 XYP sing 371 n n C3 O3 XYP sing 372 n n C3 H3 XYP sing 373 n n C4 C5 XYP sing 374 n n C4 O4 XYP sing 375 n n C4 H4 XYP sing 376 n n C5 O5 XYP sing 377 n n C5 H51 XYP sing 378 n n C5 H52 XYP sing 379 n n O2 HO2 XYP sing 380 n n O3 HO3 XYP sing 381 n n O4 HO4 XYP sing 382 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 XYP DXylpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 XYP b-D-xylopyranose 'COMMON NAME' GMML 1 XYP b-D-Xylp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 XYP Xyl 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4XUQ _atom_sites.fract_transf_matrix[1][1] 0.010816 _atom_sites.fract_transf_matrix[1][2] 0.006245 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012489 _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] 0.020651 _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 E 3 XYP A 1 1001 1001 XYP XYP . F 4 CA A 1 1004 1101 CA CA . G 3 XYP B 1 401 1002 XYP XYP . H 3 XYP B 1 402 1003 XYP XYP . I 4 CA B 1 403 1101 CA CA . J 3 XYP C 1 401 1002 XYP XYP . K 3 XYP C 1 402 1003 XYP XYP . L 4 CA C 1 403 1101 CA CA . M 5 HOH A 1 1101 48 HOH HOH . M 5 HOH A 2 1102 12 HOH HOH . M 5 HOH A 3 1103 46 HOH HOH . M 5 HOH A 4 1104 63 HOH HOH . M 5 HOH A 5 1105 77 HOH HOH . M 5 HOH A 6 1106 50 HOH HOH . M 5 HOH A 7 1107 28 HOH HOH . M 5 HOH A 8 1108 68 HOH HOH . M 5 HOH A 9 1109 6 HOH HOH . M 5 HOH A 10 1110 31 HOH HOH . M 5 HOH A 11 1111 24 HOH HOH . M 5 HOH A 12 1112 44 HOH HOH . M 5 HOH A 13 1113 72 HOH HOH . M 5 HOH A 14 1114 16 HOH HOH . M 5 HOH A 15 1115 18 HOH HOH . M 5 HOH A 16 1116 35 HOH HOH . M 5 HOH A 17 1117 11 HOH HOH . M 5 HOH A 18 1118 42 HOH HOH . M 5 HOH A 19 1119 1 HOH HOH . M 5 HOH A 20 1120 13 HOH HOH . M 5 HOH A 21 1121 8 HOH HOH . M 5 HOH A 22 1122 62 HOH HOH . M 5 HOH A 23 1123 29 HOH HOH . M 5 HOH A 24 1124 25 HOH HOH . M 5 HOH A 25 1125 23 HOH HOH . M 5 HOH A 26 1126 84 HOH HOH . M 5 HOH A 27 1127 56 HOH HOH . M 5 HOH A 28 1128 10 HOH HOH . M 5 HOH A 29 1129 76 HOH HOH . M 5 HOH A 30 1130 80 HOH HOH . M 5 HOH A 31 1131 30 HOH HOH . M 5 HOH A 32 1132 55 HOH HOH . M 5 HOH A 33 1133 74 HOH HOH . M 5 HOH A 34 1134 17 HOH HOH . M 5 HOH A 35 1135 7 HOH HOH . N 5 HOH B 1 501 69 HOH HOH . N 5 HOH B 2 502 15 HOH HOH . N 5 HOH B 3 503 45 HOH HOH . N 5 HOH B 4 504 54 HOH HOH . N 5 HOH B 5 505 27 HOH HOH . N 5 HOH B 6 506 47 HOH HOH . N 5 HOH B 7 507 82 HOH HOH . N 5 HOH B 8 508 40 HOH HOH . N 5 HOH B 9 509 64 HOH HOH . N 5 HOH B 10 510 9 HOH HOH . N 5 HOH B 11 511 53 HOH HOH . N 5 HOH B 12 512 81 HOH HOH . N 5 HOH B 13 513 61 HOH HOH . N 5 HOH B 14 514 71 HOH HOH . N 5 HOH B 15 515 43 HOH HOH . N 5 HOH B 16 516 3 HOH HOH . N 5 HOH B 17 517 57 HOH HOH . N 5 HOH B 18 518 2 HOH HOH . N 5 HOH B 19 519 41 HOH HOH . N 5 HOH B 20 520 73 HOH HOH . N 5 HOH B 21 521 32 HOH HOH . N 5 HOH B 22 522 58 HOH HOH . N 5 HOH B 23 523 70 HOH HOH . N 5 HOH B 24 524 49 HOH HOH . O 5 HOH C 1 501 85 HOH HOH . O 5 HOH C 2 502 22 HOH HOH . O 5 HOH C 3 503 67 HOH HOH . O 5 HOH C 4 504 33 HOH HOH . O 5 HOH C 5 505 66 HOH HOH . O 5 HOH C 6 506 65 HOH HOH . O 5 HOH C 7 507 59 HOH HOH . O 5 HOH C 8 508 26 HOH HOH . O 5 HOH C 9 509 14 HOH HOH . O 5 HOH C 10 510 83 HOH HOH . O 5 HOH C 11 511 51 HOH HOH . O 5 HOH C 12 512 52 HOH HOH . O 5 HOH C 13 513 19 HOH HOH . O 5 HOH C 14 514 60 HOH HOH . O 5 HOH C 15 515 34 HOH HOH . O 5 HOH C 16 516 4 HOH HOH . O 5 HOH C 17 517 78 HOH HOH . O 5 HOH C 18 518 79 HOH HOH . O 5 HOH C 19 519 36 HOH HOH . O 5 HOH C 20 520 75 HOH HOH . O 5 HOH C 21 521 37 HOH HOH . O 5 HOH C 22 522 38 HOH HOH . O 5 HOH C 23 523 39 HOH HOH . O 5 HOH C 24 524 5 HOH HOH . O 5 HOH C 25 525 21 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 XYP . . . G 3 -40.848 -12.922 -6.646 1 35.79 ? C1 XYP 401 B 1 HETATM 2 C C2 XYP . . . G 3 -42.062 -12.042 -6.324 1 36.81 ? C2 XYP 401 B 1 HETATM 3 C C3 XYP . . . G 3 -43.277 -12.787 -6.87 1 40.28 ? C3 XYP 401 B 1 HETATM 4 C C4 XYP . . . G 3 -43.056 -13.147 -8.355 1 40.75 ? C4 XYP 401 B 1 HETATM 5 C C5 XYP . . . G 3 -41.733 -13.853 -8.582 1 35.76 ? C5 XYP 401 B 1 HETATM 6 O O2 XYP . . . G 3 -42.097 -11.789 -4.907 1 33.84 ? O2 XYP 401 B 1 HETATM 7 O O3 XYP . . . G 3 -44.425 -11.957 -6.693 1 36.01 ? O3 XYP 401 B 1 HETATM 8 O O4 XYP . . . G 3 -44.114 -13.973 -8.772 1 42.87 ? O4 XYP 401 B 1 HETATM 9 O O5 XYP . . . G 3 -40.718 -13.003 -8.062 1 41.61 ? O5 XYP 401 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 9 #