data_4RYK # _model_server_result.job_id a38QzCQIlioMMOhaRhZRFA _model_server_result.datetime_utc '2025-08-31 04:21:14' _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 4ryk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 4RYK # _exptl.entry_id 4RYK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 106.12 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DI(HYDROXYETHYL)ETHER _entity.pdbx_number_of_molecules 1 _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 4RYK _cell.length_a 86.31 _cell.length_b 103.93 _cell.length_c 112.81 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RYK _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 21 21' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_566 x,-y+1,-z+3/2 1 0 0 0 -1 0 0 0 -1 0 103.93 169.215 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _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 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _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 B GLC 1 B 1 GLC B 1 SUC 2 n B FRU 2 B 2 FRU B 1 SUC # 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 ILE 60 A ILE 54 1_555 A N MSE 61 A MSE 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale2 A C MSE 61 A MSE 55 1_555 A N VAL 62 A VAL 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale3 A C GLY 97 A GLY 91 1_555 A N MSE 98 A MSE 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 A C MSE 98 A MSE 92 1_555 A N GLN 99 A GLN 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale5 A C LYS 155 A LYS 149 1_555 A N MSE 156 A MSE 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale6 A C MSE 156 A MSE 150 1_555 A N GLN 157 A GLN 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.308 ? covale ? covale7 A C ILE 185 A ILE 179 1_555 A N MSE 186 A MSE 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale8 A C MSE 186 A MSE 180 1_555 A N LEU 187 A LEU 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale9 A C TRP 257 A TRP 251 1_555 A N MSE 258 A MSE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 A C MSE 258 A MSE 252 1_555 A N LYS 259 A LYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale11 B C1 GLC . B GLC 1 1_555 B O2 FRU . B FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 sing # _chem_comp.formula 'C4 H10 O3' _chem_comp.formula_weight 106.12 _chem_comp.id PEG _chem_comp.mon_nstd_flag . _chem_comp.name DI(HYDROXYETHYL)ETHER _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O1 PEG sing 285 n n C1 C2 PEG sing 286 n n C1 H11 PEG sing 287 n n C1 H12 PEG sing 288 n n O1 HO1 PEG sing 289 n n C2 O2 PEG sing 290 n n C2 H21 PEG sing 291 n n C2 H22 PEG sing 292 n n O2 C3 PEG sing 293 n n C3 C4 PEG sing 294 n n C3 H31 PEG sing 295 n n C3 H32 PEG sing 296 n n C4 O4 PEG sing 297 n n C4 H41 PEG sing 298 n n C4 H42 PEG sing 299 n n O4 HO4 PEG sing 300 n n # _atom_sites.entry_id 4RYK _atom_sites.fract_transf_matrix[1][1] 0.011586 _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] 0.009622 _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] 0.008864 _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 TLA A 1 402 1 TLA TLA . D 4 PEG A 1 403 1 PEG PEG . E 5 HOH A 1 501 1 HOH HOH . E 5 HOH A 2 502 2 HOH HOH . E 5 HOH A 3 503 3 HOH HOH . E 5 HOH A 4 504 4 HOH HOH . E 5 HOH A 5 505 5 HOH HOH . E 5 HOH A 6 506 6 HOH HOH . E 5 HOH A 7 507 7 HOH HOH . E 5 HOH A 8 508 8 HOH HOH . E 5 HOH A 9 509 10 HOH HOH . E 5 HOH A 10 510 11 HOH HOH . E 5 HOH A 11 511 12 HOH HOH . E 5 HOH A 12 512 13 HOH HOH . E 5 HOH A 13 513 14 HOH HOH . E 5 HOH A 14 514 15 HOH HOH . E 5 HOH A 15 515 16 HOH HOH . E 5 HOH A 16 516 18 HOH HOH . E 5 HOH A 17 517 19 HOH HOH . E 5 HOH A 18 518 20 HOH HOH . E 5 HOH A 19 519 21 HOH HOH . E 5 HOH A 20 520 22 HOH HOH . E 5 HOH A 21 521 23 HOH HOH . E 5 HOH A 22 522 24 HOH HOH . E 5 HOH A 23 523 25 HOH HOH . E 5 HOH A 24 524 26 HOH HOH . E 5 HOH A 25 525 27 HOH HOH . E 5 HOH A 26 526 28 HOH HOH . E 5 HOH A 27 527 29 HOH HOH . E 5 HOH A 28 528 30 HOH HOH . E 5 HOH A 29 529 31 HOH HOH . E 5 HOH A 30 530 32 HOH HOH . E 5 HOH A 31 531 33 HOH HOH . E 5 HOH A 32 532 34 HOH HOH . E 5 HOH A 33 533 35 HOH HOH . E 5 HOH A 34 534 36 HOH HOH . E 5 HOH A 35 535 37 HOH HOH . E 5 HOH A 36 536 38 HOH HOH . E 5 HOH A 37 537 40 HOH HOH . E 5 HOH A 38 538 41 HOH HOH . E 5 HOH A 39 539 42 HOH HOH . E 5 HOH A 40 540 43 HOH HOH . E 5 HOH A 41 541 44 HOH HOH . E 5 HOH A 42 542 45 HOH HOH . E 5 HOH A 43 543 48 HOH HOH . E 5 HOH A 44 544 49 HOH HOH . E 5 HOH A 45 545 50 HOH HOH . E 5 HOH A 46 546 51 HOH HOH . E 5 HOH A 47 547 53 HOH HOH . E 5 HOH A 48 548 54 HOH HOH . E 5 HOH A 49 549 55 HOH HOH . E 5 HOH A 50 550 56 HOH HOH . E 5 HOH A 51 551 57 HOH HOH . E 5 HOH A 52 552 58 HOH HOH . E 5 HOH A 53 553 59 HOH HOH . E 5 HOH A 54 554 62 HOH HOH . E 5 HOH A 55 555 63 HOH HOH . E 5 HOH A 56 556 65 HOH HOH . E 5 HOH A 57 557 66 HOH HOH . E 5 HOH A 58 558 69 HOH HOH . E 5 HOH A 59 559 72 HOH HOH . E 5 HOH A 60 560 74 HOH HOH . E 5 HOH A 61 561 76 HOH HOH . E 5 HOH A 62 562 77 HOH HOH . E 5 HOH A 63 563 78 HOH HOH . E 5 HOH A 64 564 79 HOH HOH . E 5 HOH A 65 565 80 HOH HOH . E 5 HOH A 66 566 83 HOH HOH . E 5 HOH A 67 567 86 HOH HOH . E 5 HOH A 68 568 87 HOH HOH . E 5 HOH A 69 569 89 HOH HOH . E 5 HOH A 70 570 91 HOH HOH . E 5 HOH A 71 571 92 HOH HOH . E 5 HOH A 72 572 96 HOH HOH . E 5 HOH A 73 573 97 HOH HOH . E 5 HOH A 74 574 99 HOH HOH . E 5 HOH A 75 575 102 HOH HOH . E 5 HOH A 76 576 104 HOH HOH . E 5 HOH A 77 577 106 HOH HOH . E 5 HOH A 78 578 108 HOH HOH . E 5 HOH A 79 579 110 HOH HOH . E 5 HOH A 80 580 111 HOH HOH . E 5 HOH A 81 581 112 HOH HOH . E 5 HOH A 82 582 114 HOH HOH . E 5 HOH A 83 583 115 HOH HOH . E 5 HOH A 84 584 119 HOH HOH . E 5 HOH A 85 585 123 HOH HOH . E 5 HOH A 86 586 124 HOH HOH . E 5 HOH A 87 587 125 HOH HOH . E 5 HOH A 88 588 127 HOH HOH . E 5 HOH A 89 589 131 HOH HOH . E 5 HOH A 90 590 135 HOH HOH . E 5 HOH A 91 591 136 HOH HOH . E 5 HOH A 92 592 138 HOH HOH . E 5 HOH A 93 593 140 HOH HOH . E 5 HOH A 94 594 143 HOH HOH . E 5 HOH A 95 595 149 HOH HOH . E 5 HOH A 96 596 153 HOH HOH . E 5 HOH A 97 597 154 HOH HOH . E 5 HOH A 98 598 159 HOH HOH . E 5 HOH A 99 599 163 HOH HOH . E 5 HOH A 100 600 168 HOH HOH . E 5 HOH A 101 601 174 HOH HOH . E 5 HOH A 102 602 182 HOH HOH . E 5 HOH A 103 603 205 HOH HOH . E 5 HOH A 104 604 210 HOH HOH . E 5 HOH A 105 605 212 HOH HOH . E 5 HOH A 106 606 213 HOH HOH . E 5 HOH A 107 607 214 HOH HOH . E 5 HOH A 108 608 215 HOH HOH . E 5 HOH A 109 609 216 HOH HOH . E 5 HOH A 110 610 217 HOH HOH . E 5 HOH A 111 611 218 HOH HOH . E 5 HOH A 112 612 219 HOH HOH . E 5 HOH A 113 613 220 HOH HOH . E 5 HOH A 114 614 221 HOH HOH . E 5 HOH A 115 615 222 HOH HOH . E 5 HOH A 116 616 224 HOH HOH . E 5 HOH A 117 617 225 HOH HOH . E 5 HOH A 118 618 226 HOH HOH . E 5 HOH A 119 619 228 HOH HOH . E 5 HOH A 120 620 229 HOH HOH . E 5 HOH A 121 621 230 HOH HOH . E 5 HOH A 122 622 231 HOH HOH . E 5 HOH A 123 623 232 HOH HOH . E 5 HOH A 124 624 233 HOH HOH . E 5 HOH A 125 625 234 HOH HOH . E 5 HOH A 126 626 235 HOH HOH . E 5 HOH A 127 627 236 HOH HOH . E 5 HOH A 128 628 237 HOH HOH . E 5 HOH A 129 629 238 HOH HOH . E 5 HOH A 130 630 239 HOH HOH . E 5 HOH A 131 631 240 HOH HOH . E 5 HOH A 132 632 241 HOH HOH . E 5 HOH A 133 633 242 HOH HOH . E 5 HOH A 134 634 243 HOH HOH . E 5 HOH A 135 635 244 HOH HOH . E 5 HOH A 136 636 245 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 PEG . . . D 4 43.772 54.53 58.165 1 70.9 ? C1 PEG 403 A 1 HETATM 2 O O1 PEG . . . D 4 44.028 54.252 56.773 1 72.78 ? O1 PEG 403 A 1 HETATM 3 C C2 PEG . . . D 4 43.157 55.914 58.385 1 71.65 ? C2 PEG 403 A 1 HETATM 4 O O2 PEG . . . D 4 43.654 56.517 59.594 1 67.86 ? O2 PEG 403 A 1 HETATM 5 C C3 PEG . . . D 4 43.43 57.906 59.816 1 56.85 ? C3 PEG 403 A 1 HETATM 6 C C4 PEG . . . D 4 44.717 58.518 60.347 1 62.79 ? C4 PEG 403 A 1 HETATM 7 O O4 PEG . . . D 4 44.794 59.94 60.124 1 63.37 ? O4 PEG 403 A 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 598 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 7 #