data_5OT3 # _model_server_result.job_id aS0irSTVzLNfRkRtG33U_Q _model_server_result.datetime_utc '2024-11-22 11:29:51' _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 5ot3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 5OT3 # _exptl.entry_id 5OT3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-ribopyranose _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 5OT3 _cell.length_a 69.21 _cell.length_b 72.752 _cell.length_c 76.925 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OT3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 PHE 141 A PHE 138 1_555 A N SEP 142 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C SEP 142 A SEP 139 1_555 A N GLU 143 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C TRP 199 A TRP 196 1_555 A N TPO 200 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale4 A C TPO 200 A TPO 197 1_555 A N LEU 201 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C VAL 340 A VAL 337 1_555 A N SEP 341 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C SEP 341 A SEP 338 1_555 A N ILE 342 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 B OG SER 17 D SER 24 1_555 E C1 RIP . D RIP 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? # _chem_comp.formula 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id RIP _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-ribopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms 'beta-D-ribose;D-ribose;ribose;RIBOSE(PYRANOSE FORM)' # 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 RIP sing 355 n n C1 O1 RIP sing 356 n n C1 O5 RIP sing 357 n n C1 H1 RIP sing 358 n n C2 C3 RIP sing 359 n n C2 O2 RIP sing 360 n n C2 H2 RIP sing 361 n n C3 C4 RIP sing 362 n n C3 O3 RIP sing 363 n n C3 H3 RIP sing 364 n n C4 C5 RIP sing 365 n n C4 O4 RIP sing 366 n n C4 H4 RIP sing 367 n n C5 O5 RIP sing 368 n n C5 H51 RIP sing 369 n n C5 H52 RIP sing 370 n n O1 HO1 RIP sing 371 n n O2 HO2 RIP sing 372 n n O3 HO3 RIP sing 373 n n O4 HO4 RIP sing 374 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 RIP DRibpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 RIP b-D-ribopyranose 'COMMON NAME' GMML 1 RIP b-D-Ribp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 RIP Rib 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5OT3 _atom_sites.fract_transf_matrix[1][1] 0.014449 _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] 0.013745 _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] 0.013 _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 9LQ A 1 401 1 9LQ BFS . D 4 MPD A 1 402 1 MPD MPD . E 5 RIP D 1 101 1 RIP RIB . F 6 CL D 1 102 1 CL CL . G 7 HOH A 1 501 31 HOH HOH . G 7 HOH A 2 502 93 HOH HOH . G 7 HOH A 3 503 61 HOH HOH . G 7 HOH A 4 504 67 HOH HOH . G 7 HOH A 5 505 11 HOH HOH . G 7 HOH A 6 506 102 HOH HOH . G 7 HOH A 7 507 17 HOH HOH . G 7 HOH A 8 508 27 HOH HOH . G 7 HOH A 9 509 96 HOH HOH . G 7 HOH A 10 510 13 HOH HOH . G 7 HOH A 11 511 63 HOH HOH . G 7 HOH A 12 512 46 HOH HOH . G 7 HOH A 13 513 109 HOH HOH . G 7 HOH A 14 514 85 HOH HOH . G 7 HOH A 15 515 110 HOH HOH . G 7 HOH A 16 516 60 HOH HOH . G 7 HOH A 17 517 72 HOH HOH . G 7 HOH A 18 518 4 HOH HOH . G 7 HOH A 19 519 124 HOH HOH . G 7 HOH A 20 520 3 HOH HOH . G 7 HOH A 21 521 25 HOH HOH . G 7 HOH A 22 522 105 HOH HOH . G 7 HOH A 23 523 38 HOH HOH . G 7 HOH A 24 524 18 HOH HOH . G 7 HOH A 25 525 92 HOH HOH . G 7 HOH A 26 526 8 HOH HOH . G 7 HOH A 27 527 45 HOH HOH . G 7 HOH A 28 528 66 HOH HOH . G 7 HOH A 29 529 10 HOH HOH . G 7 HOH A 30 530 121 HOH HOH . G 7 HOH A 31 531 91 HOH HOH . G 7 HOH A 32 532 64 HOH HOH . G 7 HOH A 33 533 98 HOH HOH . G 7 HOH A 34 534 2 HOH HOH . G 7 HOH A 35 535 44 HOH HOH . G 7 HOH A 36 536 12 HOH HOH . G 7 HOH A 37 537 115 HOH HOH . G 7 HOH A 38 538 39 HOH HOH . G 7 HOH A 39 539 33 HOH HOH . G 7 HOH A 40 540 32 HOH HOH . G 7 HOH A 41 541 54 HOH HOH . G 7 HOH A 42 542 73 HOH HOH . G 7 HOH A 43 543 95 HOH HOH . G 7 HOH A 44 544 26 HOH HOH . G 7 HOH A 45 545 23 HOH HOH . G 7 HOH A 46 546 14 HOH HOH . G 7 HOH A 47 547 48 HOH HOH . G 7 HOH A 48 548 7 HOH HOH . G 7 HOH A 49 549 104 HOH HOH . G 7 HOH A 50 550 52 HOH HOH . G 7 HOH A 51 551 50 HOH HOH . G 7 HOH A 52 552 78 HOH HOH . G 7 HOH A 53 553 107 HOH HOH . G 7 HOH A 54 554 21 HOH HOH . G 7 HOH A 55 555 9 HOH HOH . G 7 HOH A 56 556 83 HOH HOH . G 7 HOH A 57 557 69 HOH HOH . G 7 HOH A 58 558 76 HOH HOH . G 7 HOH A 59 559 30 HOH HOH . G 7 HOH A 60 560 43 HOH HOH . G 7 HOH A 61 561 103 HOH HOH . G 7 HOH A 62 562 94 HOH HOH . G 7 HOH A 63 563 90 HOH HOH . G 7 HOH A 64 564 34 HOH HOH . G 7 HOH A 65 565 88 HOH HOH . G 7 HOH A 66 566 59 HOH HOH . G 7 HOH A 67 567 77 HOH HOH . G 7 HOH A 68 568 86 HOH HOH . G 7 HOH A 69 569 71 HOH HOH . G 7 HOH A 70 570 15 HOH HOH . G 7 HOH A 71 571 99 HOH HOH . G 7 HOH A 72 572 101 HOH HOH . G 7 HOH A 73 573 41 HOH HOH . G 7 HOH A 74 574 36 HOH HOH . G 7 HOH A 75 575 70 HOH HOH . G 7 HOH A 76 576 22 HOH HOH . G 7 HOH A 77 577 53 HOH HOH . G 7 HOH A 78 578 16 HOH HOH . G 7 HOH A 79 579 80 HOH HOH . G 7 HOH A 80 580 79 HOH HOH . G 7 HOH A 81 581 89 HOH HOH . G 7 HOH A 82 582 82 HOH HOH . G 7 HOH A 83 583 37 HOH HOH . G 7 HOH A 84 584 29 HOH HOH . G 7 HOH A 85 585 62 HOH HOH . H 7 HOH D 1 201 28 HOH HOH . H 7 HOH D 2 202 6 HOH HOH . H 7 HOH D 3 203 112 HOH HOH . H 7 HOH D 4 204 74 HOH HOH . H 7 HOH D 5 205 122 HOH HOH . H 7 HOH D 6 206 123 HOH HOH . H 7 HOH D 7 207 114 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 RIP . . . E 5 -2.326 19.956 11.596 1 72.76 ? C1 RIP 101 D 1 HETATM 2 C C2 RIP . . . E 5 -2.085 19.251 10.259 1 71.25 ? C2 RIP 101 D 1 HETATM 3 C C3 RIP . . . E 5 -3.412 18.93 9.581 1 70.59 ? C3 RIP 101 D 1 HETATM 4 C C4 RIP . . . E 5 -4.358 20.121 9.626 1 74.62 ? C4 RIP 101 D 1 HETATM 5 C C5 RIP . . . E 5 -3.605 21.346 10.112 1 76.28 ? C5 RIP 101 D 1 HETATM 6 O O5 RIP . . . E 5 -3.091 21.153 11.438 1 74.1 ? O5 RIP 101 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 407 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #