data_4XUR # _model_server_result.job_id E07Co6wgfYh-T_eETPvn-g _model_server_result.datetime_utc '2025-04-06 11:16:15' _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 4xur # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1004}' # _entry.id 4XUR # _exptl.entry_id 4XUR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 6 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description beta-D-xylopyranose _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 120 _cell.entry_id 4XUR _cell.length_a 92.769 _cell.length_b 92.769 _cell.length_c 48.571 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XUR _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,G,L 1 1 B,E,H,I,M 2 1 C,F,J,K,N 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 ? 6 H N N ? 6 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 2 2 1 XYP XYP C1 O1 . O4 HO4 . sing 2 ? 2 3 2 XYP XYP C1 O1 . O4 HO4 . sing 3 ? 2 4 3 XYP XYP C1 O1 . O4 HO4 . sing 4 ? 3 2 1 XYP XYP C1 O1 . O4 HO4 . sing 5 ? 4 2 1 XYP XYP C1 O1 . O4 HO4 . sing 6 ? 4 3 2 XYP XYP C1 O1 . O4 HO4 . 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 1001 XYP 2 n D XYP 2 D 2 XYP A 1002 XYP 2 n D XYP 3 D 3 XYP A 1003 XYP 2 n D XYP 4 D 4 XYP A 1004 XYP 3 n E XYP 1 E 1 XYP B 1001 XYP 3 n E XYP 2 E 2 XYP B 1002 XYP 4 n F XYP 1 F 1 XYP C 1001 XYP 4 n F XYP 2 F 2 XYP C 1002 XYP 4 n F XYP 3 F 3 XYP C 1003 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.534 ? covale ? covale2 D O4 XYP . D XYP 2 1_555 D C1 XYP . D XYP 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale3 D O4 XYP . D XYP 3 1_555 D C1 XYP . D XYP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale4 E O4 XYP . E XYP 1 1_555 E C1 XYP . E XYP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale5 F O4 XYP . F XYP 1 1_555 F C1 XYP . F XYP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.515 ? covale ? covale6 F O4 XYP . F XYP 2 1_555 F C1 XYP . F XYP 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? metalc ? metalc1 A O ASP 19 A ASP 177 1_555 G CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc2 A OE2 GLU 21 A GLU 179 1_555 G CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc3 A OG SER 46 A SER 204 1_555 G CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc4 A O ARG 48 A ARG 206 1_555 G CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc5 A OD1 ASP 167 A ASP 325 1_555 G CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 A OD2 ASP 167 A ASP 325 1_555 G CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc7 G CA CA . A CA 1005 1_555 L O HOH . A HOH 1133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc8 B O ASP 19 B ASP 177 1_555 I CA CA . B CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc9 B OE2 GLU 21 B GLU 179 1_555 I CA CA . B CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc10 B OG SER 46 B SER 204 1_555 I CA CA . B CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc11 B O ARG 48 B ARG 206 1_555 I CA CA . B CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc12 B OD1 ASP 167 B ASP 325 1_555 I CA CA . B CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc13 B OD2 ASP 167 B ASP 325 1_555 I CA CA . B CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc14 I CA CA . B CA 1004 1_555 M O HOH . B HOH 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc15 C O ASP 19 C ASP 177 1_555 K CA CA . C CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc16 C OE2 GLU 21 C GLU 179 1_555 K CA CA . C CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc17 C OG SER 46 C SER 204 1_555 K CA CA . C CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc18 C O ARG 48 C ARG 206 1_555 K CA CA . C CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc19 C OD1 ASP 167 C ASP 325 1_555 K CA CA . C CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc20 C OD2 ASP 167 C ASP 325 1_555 K CA CA . C CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc21 K CA CA . C CA 1005 1_555 N O HOH . C HOH 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? # _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 4XUR _atom_sites.fract_transf_matrix[1][1] 0.010779 _atom_sites.fract_transf_matrix[1][2] 0.006224 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012447 _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] 0.020589 _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 5 CA A 1 1005 1101 CA CA . H 6 XYP B 1 1003 1003 XYP XYP . I 5 CA B 1 1004 1101 CA CA . J 6 XYP C 1 1004 1004 XYP XYP . K 5 CA C 1 1005 1104 CA CA . L 7 HOH A 1 1101 34 HOH HOH . L 7 HOH A 2 1102 43 HOH HOH . L 7 HOH A 3 1103 71 HOH HOH . L 7 HOH A 4 1104 18 HOH HOH . L 7 HOH A 5 1105 49 HOH HOH . L 7 HOH A 6 1106 55 HOH HOH . L 7 HOH A 7 1107 64 HOH HOH . L 7 HOH A 8 1108 13 HOH HOH . L 7 HOH A 9 1109 3 HOH HOH . L 7 HOH A 10 1110 82 HOH HOH . L 7 HOH A 11 1111 32 HOH HOH . L 7 HOH A 12 1112 40 HOH HOH . L 7 HOH A 13 1113 52 HOH HOH . L 7 HOH A 14 1114 4 HOH HOH . L 7 HOH A 15 1115 8 HOH HOH . L 7 HOH A 16 1116 12 HOH HOH . L 7 HOH A 17 1117 20 HOH HOH . L 7 HOH A 18 1118 25 HOH HOH . L 7 HOH A 19 1119 26 HOH HOH . L 7 HOH A 20 1120 35 HOH HOH . L 7 HOH A 21 1121 38 HOH HOH . L 7 HOH A 22 1122 50 HOH HOH . L 7 HOH A 23 1123 68 HOH HOH . L 7 HOH A 24 1124 74 HOH HOH . L 7 HOH A 25 1125 75 HOH HOH . L 7 HOH A 26 1126 79 HOH HOH . L 7 HOH A 27 1127 80 HOH HOH . L 7 HOH A 28 1128 84 HOH HOH . L 7 HOH A 29 1129 86 HOH HOH . L 7 HOH A 30 1130 89 HOH HOH . L 7 HOH A 31 1131 91 HOH HOH . L 7 HOH A 32 1132 93 HOH HOH . L 7 HOH A 33 1133 96 HOH HOH . M 7 HOH B 1 1101 76 HOH HOH . M 7 HOH B 2 1102 7 HOH HOH . M 7 HOH B 3 1103 60 HOH HOH . M 7 HOH B 4 1104 78 HOH HOH . M 7 HOH B 5 1105 85 HOH HOH . M 7 HOH B 6 1106 29 HOH HOH . M 7 HOH B 7 1107 22 HOH HOH . M 7 HOH B 8 1108 17 HOH HOH . M 7 HOH B 9 1109 24 HOH HOH . M 7 HOH B 10 1110 16 HOH HOH . M 7 HOH B 11 1111 10 HOH HOH . M 7 HOH B 12 1112 6 HOH HOH . M 7 HOH B 13 1113 56 HOH HOH . M 7 HOH B 14 1114 51 HOH HOH . M 7 HOH B 15 1115 87 HOH HOH . M 7 HOH B 16 1116 5 HOH HOH . M 7 HOH B 17 1117 11 HOH HOH . M 7 HOH B 18 1118 14 HOH HOH . M 7 HOH B 19 1119 23 HOH HOH . M 7 HOH B 20 1120 27 HOH HOH . M 7 HOH B 21 1121 28 HOH HOH . M 7 HOH B 22 1122 33 HOH HOH . M 7 HOH B 23 1123 41 HOH HOH . M 7 HOH B 24 1124 58 HOH HOH . M 7 HOH B 25 1125 61 HOH HOH . M 7 HOH B 26 1126 69 HOH HOH . M 7 HOH B 27 1127 70 HOH HOH . M 7 HOH B 28 1128 88 HOH HOH . M 7 HOH B 29 1129 90 HOH HOH . M 7 HOH B 30 1130 92 HOH HOH . N 7 HOH C 1 1101 65 HOH HOH . N 7 HOH C 2 1102 21 HOH HOH . N 7 HOH C 3 1103 15 HOH HOH . N 7 HOH C 4 1104 53 HOH HOH . N 7 HOH C 5 1105 94 HOH HOH . N 7 HOH C 6 1106 83 HOH HOH . N 7 HOH C 7 1107 9 HOH HOH . N 7 HOH C 8 1108 39 HOH HOH . N 7 HOH C 9 1109 66 HOH HOH . N 7 HOH C 10 1110 48 HOH HOH . N 7 HOH C 11 1111 62 HOH HOH . N 7 HOH C 12 1112 57 HOH HOH . N 7 HOH C 13 1113 67 HOH HOH . N 7 HOH C 14 1114 19 HOH HOH . N 7 HOH C 15 1115 30 HOH HOH . N 7 HOH C 16 1116 31 HOH HOH . N 7 HOH C 17 1117 36 HOH HOH . N 7 HOH C 18 1118 37 HOH HOH . N 7 HOH C 19 1119 42 HOH HOH . N 7 HOH C 20 1120 44 HOH HOH . N 7 HOH C 21 1121 45 HOH HOH . N 7 HOH C 22 1122 46 HOH HOH . N 7 HOH C 23 1123 47 HOH HOH . N 7 HOH C 24 1124 54 HOH HOH . N 7 HOH C 25 1125 59 HOH HOH . N 7 HOH C 26 1126 63 HOH HOH . N 7 HOH C 27 1127 72 HOH HOH . N 7 HOH C 28 1128 73 HOH HOH . N 7 HOH C 29 1129 77 HOH HOH . N 7 HOH C 30 1130 81 HOH HOH . N 7 HOH C 31 1131 95 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 . . . J 6 58.082 20.849 2.248 1 27.1 ? C1 XYP 1004 C 1 HETATM 2 C C2 XYP . . . J 6 56.647 20.561 2.649 1 28.11 ? C2 XYP 1004 C 1 HETATM 3 C C3 XYP . . . J 6 56.669 20.225 4.119 1 28.77 ? C3 XYP 1004 C 1 HETATM 4 C C4 XYP . . . J 6 57.744 19.192 4.44 1 29.95 ? C4 XYP 1004 C 1 HETATM 5 C C5 XYP . . . J 6 59.11 19.584 3.9 1 29.14 ? C5 XYP 1004 C 1 HETATM 6 O O2 XYP . . . J 6 55.841 21.722 2.371 1 26.05 ? O2 XYP 1004 C 1 HETATM 7 O O3 XYP . . . J 6 55.363 19.788 4.518 1 30.39 ? O3 XYP 1004 C 1 HETATM 8 O O4 XYP . . . J 6 57.884 19.114 5.872 1 31.54 ? O4 XYP 1004 C 1 HETATM 9 O O5 XYP . . . J 6 58.997 19.818 2.515 1 32.31 ? O5 XYP 1004 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 9 #