data_4YWH # _model_server_result.job_id 6X8Tl1i-ll5P2b0Qkcz7zg _model_server_result.datetime_utc '2024-12-26 12:09:19' _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 4ywh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4YWH # _exptl.entry_id 4YWH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 2 _entity.src_method man _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 91.5 _cell.angle_gamma 90 _cell.entry_id 4YWH _cell.length_a 80.796 _cell.length_b 37.67 _cell.length_c 105.336 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YWH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 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 ? 2 C N N ? 2 D 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 covale ? covale1 A C MSE 23 A MSE 23 1_555 A N LYS 24 A LYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C GLY 29 A GLY 29 1_555 A N MSE 30 A MSE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 A C MSE 30 A MSE 30 1_555 A N SER 31 A SER 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C ASN 76 A ASN 76 1_555 A N MSE 77 A MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale5 A C MSE 77 A MSE 77 1_555 A N LEU 78 A LEU 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale6 A C LEU 151 A LEU 151 1_555 A N MSE 152 A MSE 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale7 A C MSE 152 A MSE 152 1_555 A N GLY 153 A GLY 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale8 A C GLN 168 A GLN 168 1_555 A N MSE 169 A MSE 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale9 A C MSE 169 A MSE 169 1_555 A N LYS 170 A LYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale10 A C ILE 200 A ILE 200 1_555 A N MSE 201 A MSE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 A C MSE 201 A MSE 201 1_555 A N GLU 202 A GLU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale12 A C THR 260 A THR 260 1_555 A N MSE 261 A MSE 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale13 A C MSE 261 A MSE 261 1_555 A N THR 262 A THR 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale14 B C GLY 29 B GLY 29 1_555 B N MSE 30 B MSE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale15 B C MSE 30 B MSE 30 1_555 B N SER 31 B SER 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale16 B C ASN 76 B ASN 76 1_555 B N MSE 77 B MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale17 B C MSE 77 B MSE 77 1_555 B N LEU 78 B LEU 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale18 B C LEU 151 B LEU 151 1_555 B N MSE 152 B MSE 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale19 B C MSE 152 B MSE 152 1_555 B N GLY 153 B GLY 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale20 B C GLN 168 B GLN 168 1_555 B N MSE 169 B MSE 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale21 B C MSE 169 B MSE 169 1_555 B N LYS 170 B LYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale22 B C ILE 200 B ILE 200 1_555 B N MSE 201 B MSE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale23 B C MSE 201 B MSE 201 1_555 B N GLU 202 B GLU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale24 B C THR 260 B THR 260 1_555 B N MSE 261 B MSE 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale25 B C MSE 261 B MSE 261 1_555 B N THR 262 B THR 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? # _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 4YWH _atom_sites.fract_transf_matrix[1][1] 0.012377 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000324 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026546 _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] 0.009497 _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 2 XYP A 1 401 1 XYP XYP . D 2 XYP B 1 401 2 XYP XYP . E 3 HOH A 1 501 65 HOH HOH . E 3 HOH A 2 502 37 HOH HOH . E 3 HOH A 3 503 120 HOH HOH . E 3 HOH A 4 504 162 HOH HOH . E 3 HOH A 5 505 81 HOH HOH . E 3 HOH A 6 506 64 HOH HOH . E 3 HOH A 7 507 93 HOH HOH . E 3 HOH A 8 508 78 HOH HOH . E 3 HOH A 9 509 19 HOH HOH . E 3 HOH A 10 510 7 HOH HOH . E 3 HOH A 11 511 138 HOH HOH . E 3 HOH A 12 512 59 HOH HOH . E 3 HOH A 13 513 84 HOH HOH . E 3 HOH A 14 514 26 HOH HOH . E 3 HOH A 15 515 44 HOH HOH . E 3 HOH A 16 516 54 HOH HOH . E 3 HOH A 17 517 70 HOH HOH . E 3 HOH A 18 518 67 HOH HOH . E 3 HOH A 19 519 101 HOH HOH . E 3 HOH A 20 520 60 HOH HOH . E 3 HOH A 21 521 102 HOH HOH . E 3 HOH A 22 522 79 HOH HOH . E 3 HOH A 23 523 142 HOH HOH . E 3 HOH A 24 524 16 HOH HOH . E 3 HOH A 25 525 56 HOH HOH . E 3 HOH A 26 526 57 HOH HOH . E 3 HOH A 27 527 63 HOH HOH . E 3 HOH A 28 528 39 HOH HOH . E 3 HOH A 29 529 124 HOH HOH . E 3 HOH A 30 530 169 HOH HOH . E 3 HOH A 31 531 167 HOH HOH . E 3 HOH A 32 532 118 HOH HOH . E 3 HOH A 33 533 49 HOH HOH . E 3 HOH A 34 534 139 HOH HOH . E 3 HOH A 35 535 24 HOH HOH . E 3 HOH A 36 536 28 HOH HOH . E 3 HOH A 37 537 25 HOH HOH . E 3 HOH A 38 538 72 HOH HOH . E 3 HOH A 39 539 22 HOH HOH . E 3 HOH A 40 540 171 HOH HOH . E 3 HOH A 41 541 87 HOH HOH . E 3 HOH A 42 542 144 HOH HOH . E 3 HOH A 43 543 36 HOH HOH . E 3 HOH A 44 544 41 HOH HOH . E 3 HOH A 45 545 152 HOH HOH . E 3 HOH A 46 546 147 HOH HOH . E 3 HOH A 47 547 6 HOH HOH . E 3 HOH A 48 548 145 HOH HOH . E 3 HOH A 49 549 55 HOH HOH . E 3 HOH A 50 550 160 HOH HOH . E 3 HOH A 51 551 48 HOH HOH . E 3 HOH A 52 552 31 HOH HOH . E 3 HOH A 53 553 23 HOH HOH . E 3 HOH A 54 554 10 HOH HOH . E 3 HOH A 55 555 51 HOH HOH . E 3 HOH A 56 556 53 HOH HOH . E 3 HOH A 57 557 131 HOH HOH . E 3 HOH A 58 558 35 HOH HOH . E 3 HOH A 59 559 76 HOH HOH . E 3 HOH A 60 560 11 HOH HOH . E 3 HOH A 61 561 126 HOH HOH . E 3 HOH A 62 562 104 HOH HOH . E 3 HOH A 63 563 83 HOH HOH . E 3 HOH A 64 564 110 HOH HOH . E 3 HOH A 65 565 69 HOH HOH . E 3 HOH A 66 566 180 HOH HOH . E 3 HOH A 67 567 50 HOH HOH . E 3 HOH A 68 568 141 HOH HOH . E 3 HOH A 69 569 85 HOH HOH . E 3 HOH A 70 570 116 HOH HOH . E 3 HOH A 71 571 27 HOH HOH . E 3 HOH A 72 572 181 HOH HOH . E 3 HOH A 73 573 135 HOH HOH . E 3 HOH A 74 574 159 HOH HOH . E 3 HOH A 75 575 140 HOH HOH . E 3 HOH A 76 576 179 HOH HOH . E 3 HOH A 77 577 187 HOH HOH . E 3 HOH A 78 578 113 HOH HOH . E 3 HOH A 79 579 158 HOH HOH . E 3 HOH A 80 580 178 HOH HOH . E 3 HOH A 81 581 177 HOH HOH . E 3 HOH A 82 582 172 HOH HOH . E 3 HOH A 83 583 175 HOH HOH . E 3 HOH A 84 584 133 HOH HOH . E 3 HOH A 85 585 154 HOH HOH . F 3 HOH B 1 501 91 HOH HOH . F 3 HOH B 2 502 14 HOH HOH . F 3 HOH B 3 503 105 HOH HOH . F 3 HOH B 4 504 88 HOH HOH . F 3 HOH B 5 505 77 HOH HOH . F 3 HOH B 6 506 45 HOH HOH . F 3 HOH B 7 507 71 HOH HOH . F 3 HOH B 8 508 20 HOH HOH . F 3 HOH B 9 509 122 HOH HOH . F 3 HOH B 10 510 121 HOH HOH . F 3 HOH B 11 511 12 HOH HOH . F 3 HOH B 12 512 15 HOH HOH . F 3 HOH B 13 513 8 HOH HOH . F 3 HOH B 14 514 3 HOH HOH . F 3 HOH B 15 515 174 HOH HOH . F 3 HOH B 16 516 143 HOH HOH . F 3 HOH B 17 517 62 HOH HOH . F 3 HOH B 18 518 32 HOH HOH . F 3 HOH B 19 519 42 HOH HOH . F 3 HOH B 20 520 75 HOH HOH . F 3 HOH B 21 521 95 HOH HOH . F 3 HOH B 22 522 9 HOH HOH . F 3 HOH B 23 523 109 HOH HOH . F 3 HOH B 24 524 73 HOH HOH . F 3 HOH B 25 525 34 HOH HOH . F 3 HOH B 26 526 46 HOH HOH . F 3 HOH B 27 527 52 HOH HOH . F 3 HOH B 28 528 90 HOH HOH . F 3 HOH B 29 529 89 HOH HOH . F 3 HOH B 30 530 128 HOH HOH . F 3 HOH B 31 531 100 HOH HOH . F 3 HOH B 32 532 47 HOH HOH . F 3 HOH B 33 533 112 HOH HOH . F 3 HOH B 34 534 29 HOH HOH . F 3 HOH B 35 535 82 HOH HOH . F 3 HOH B 36 536 86 HOH HOH . F 3 HOH B 37 537 166 HOH HOH . F 3 HOH B 38 538 17 HOH HOH . F 3 HOH B 39 539 151 HOH HOH . F 3 HOH B 40 540 18 HOH HOH . F 3 HOH B 41 541 153 HOH HOH . F 3 HOH B 42 542 150 HOH HOH . F 3 HOH B 43 543 146 HOH HOH . F 3 HOH B 44 544 132 HOH HOH . F 3 HOH B 45 545 92 HOH HOH . F 3 HOH B 46 546 21 HOH HOH . F 3 HOH B 47 547 13 HOH HOH . F 3 HOH B 48 548 99 HOH HOH . F 3 HOH B 49 549 173 HOH HOH . F 3 HOH B 50 550 40 HOH HOH . F 3 HOH B 51 551 149 HOH HOH . F 3 HOH B 52 552 184 HOH HOH . F 3 HOH B 53 553 96 HOH HOH . F 3 HOH B 54 554 30 HOH HOH . F 3 HOH B 55 555 43 HOH HOH . F 3 HOH B 56 556 137 HOH HOH . F 3 HOH B 57 557 61 HOH HOH . F 3 HOH B 58 558 33 HOH HOH . F 3 HOH B 59 559 125 HOH HOH . F 3 HOH B 60 560 134 HOH HOH . F 3 HOH B 61 561 97 HOH HOH . F 3 HOH B 62 562 148 HOH HOH . F 3 HOH B 63 563 66 HOH HOH . F 3 HOH B 64 564 74 HOH HOH . F 3 HOH B 65 565 94 HOH HOH . F 3 HOH B 66 566 183 HOH HOH . F 3 HOH B 67 567 119 HOH HOH . F 3 HOH B 68 568 107 HOH HOH . F 3 HOH B 69 569 58 HOH HOH . F 3 HOH B 70 570 80 HOH HOH . F 3 HOH B 71 571 127 HOH HOH . F 3 HOH B 72 572 129 HOH HOH . F 3 HOH B 73 573 163 HOH HOH . F 3 HOH B 74 574 186 HOH HOH . F 3 HOH B 75 575 185 HOH HOH . F 3 HOH B 76 576 68 HOH HOH . F 3 HOH B 77 577 38 HOH HOH . F 3 HOH B 78 578 182 HOH HOH . F 3 HOH B 79 579 123 HOH HOH . F 3 HOH B 80 580 136 HOH HOH . F 3 HOH B 81 581 108 HOH HOH . F 3 HOH B 82 582 156 HOH HOH . F 3 HOH B 83 583 106 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 O O1 XYP . . . C 2 19.332 -3.53 -2.257 1 42.89 ? O1 XYP 401 A 1 HETATM 2 C C1 XYP . . . C 2 18.144 -4.162 -2.193 1 25.95 ? C1 XYP 401 A 1 HETATM 3 C C2 XYP . . . C 2 17.077 -3.262 -2.731 1 34.14 ? C2 XYP 401 A 1 HETATM 4 C C3 XYP . . . C 2 15.827 -4.065 -2.676 1 31.82 ? C3 XYP 401 A 1 HETATM 5 C C4 XYP . . . C 2 15.982 -5.364 -3.389 1 25.02 ? C4 XYP 401 A 1 HETATM 6 C C5 XYP . . . C 2 17.113 -6.217 -2.863 1 17.95 ? C5 XYP 401 A 1 HETATM 7 O O2 XYP . . . C 2 17.059 -2.033 -1.965 1 21.98 ? O2 XYP 401 A 1 HETATM 8 O O3 XYP . . . C 2 14.849 -3.332 -3.415 1 41.31 ? O3 XYP 401 A 1 HETATM 9 O O4 XYP . . . C 2 14.826 -6.142 -3.169 1 30.75 ? O4 XYP 401 A 1 HETATM 10 O O5 XYP . . . C 2 18.272 -5.382 -3.025 1 34.53 ? O5 XYP 401 A 1 # _model_server_stats.io_time_ms 90 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #