data_6I2A # _model_server_result.job_id '_tKgMPtUi_rhOgc4VcQlgA' _model_server_result.datetime_utc '2024-10-12 20:19:48' _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 6i2a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":101}' # _entry.id 6I2A # _exptl.entry_id 6I2A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 4 _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 6I2A _cell.length_a 58.959 _cell.length_b 73.886 _cell.length_c 108.204 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6I2A _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 _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 4 _struct_asym.id D _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 GLY 12 A GLY 9 1_555 A N SEP 13 A SEP 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale2 A C SEP 13 A SEP 10 1_555 A N GLU 14 A GLU 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C PHE 141 A PHE 138 1_555 A N SEP 142 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C SEP 142 A SEP 139 1_555 A N GLU 143 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale5 A C TRP 199 A TRP 196 1_555 A N TPO 200 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale6 A C TPO 200 A TPO 197 1_555 A N LEU 201 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C VAL 340 A VAL 337 1_555 A N SEP 341 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale8 A C SEP 341 A SEP 338 1_555 A N ILE 342 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale9 B OG1 THR 12 D THR 16 1_555 D 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 ? # 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 6I2A _atom_sites.fract_transf_matrix[1][1] 0.016961 _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] 0.013534 _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] 0.009242 _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 M77 A 1 401 1 M77 FAS . D 4 RIP D 1 101 1 RIP RIB . E 5 HOH A 1 501 172 HOH HOH . E 5 HOH A 2 502 171 HOH HOH . E 5 HOH A 3 503 169 HOH HOH . E 5 HOH A 4 504 151 HOH HOH . E 5 HOH A 5 505 98 HOH HOH . E 5 HOH A 6 506 122 HOH HOH . E 5 HOH A 7 507 72 HOH HOH . E 5 HOH A 8 508 204 HOH HOH . E 5 HOH A 9 509 34 HOH HOH . E 5 HOH A 10 510 150 HOH HOH . E 5 HOH A 11 511 141 HOH HOH . E 5 HOH A 12 512 188 HOH HOH . E 5 HOH A 13 513 79 HOH HOH . E 5 HOH A 14 514 47 HOH HOH . E 5 HOH A 15 515 185 HOH HOH . E 5 HOH A 16 516 159 HOH HOH . E 5 HOH A 17 517 199 HOH HOH . E 5 HOH A 18 518 128 HOH HOH . E 5 HOH A 19 519 109 HOH HOH . E 5 HOH A 20 520 110 HOH HOH . E 5 HOH A 21 521 30 HOH HOH . E 5 HOH A 22 522 63 HOH HOH . E 5 HOH A 23 523 114 HOH HOH . E 5 HOH A 24 524 121 HOH HOH . E 5 HOH A 25 525 174 HOH HOH . E 5 HOH A 26 526 124 HOH HOH . E 5 HOH A 27 527 55 HOH HOH . E 5 HOH A 28 528 92 HOH HOH . E 5 HOH A 29 529 170 HOH HOH . E 5 HOH A 30 530 96 HOH HOH . E 5 HOH A 31 531 99 HOH HOH . E 5 HOH A 32 532 40 HOH HOH . E 5 HOH A 33 533 129 HOH HOH . E 5 HOH A 34 534 52 HOH HOH . E 5 HOH A 35 535 76 HOH HOH . E 5 HOH A 36 536 1 HOH HOH . E 5 HOH A 37 537 36 HOH HOH . E 5 HOH A 38 538 198 HOH HOH . E 5 HOH A 39 539 51 HOH HOH . E 5 HOH A 40 540 13 HOH HOH . E 5 HOH A 41 541 48 HOH HOH . E 5 HOH A 42 542 160 HOH HOH . E 5 HOH A 43 543 29 HOH HOH . E 5 HOH A 44 544 58 HOH HOH . E 5 HOH A 45 545 118 HOH HOH . E 5 HOH A 46 546 24 HOH HOH . E 5 HOH A 47 547 22 HOH HOH . E 5 HOH A 48 548 33 HOH HOH . E 5 HOH A 49 549 207 HOH HOH . E 5 HOH A 50 550 45 HOH HOH . E 5 HOH A 51 551 182 HOH HOH . E 5 HOH A 52 552 119 HOH HOH . E 5 HOH A 53 553 23 HOH HOH . E 5 HOH A 54 554 108 HOH HOH . E 5 HOH A 55 555 56 HOH HOH . E 5 HOH A 56 556 152 HOH HOH . E 5 HOH A 57 557 54 HOH HOH . E 5 HOH A 58 558 43 HOH HOH . E 5 HOH A 59 559 12 HOH HOH . E 5 HOH A 60 560 131 HOH HOH . E 5 HOH A 61 561 44 HOH HOH . E 5 HOH A 62 562 191 HOH HOH . E 5 HOH A 63 563 163 HOH HOH . E 5 HOH A 64 564 201 HOH HOH . E 5 HOH A 65 565 66 HOH HOH . E 5 HOH A 66 566 17 HOH HOH . E 5 HOH A 67 567 61 HOH HOH . E 5 HOH A 68 568 80 HOH HOH . E 5 HOH A 69 569 42 HOH HOH . E 5 HOH A 70 570 9 HOH HOH . E 5 HOH A 71 571 25 HOH HOH . E 5 HOH A 72 572 7 HOH HOH . E 5 HOH A 73 573 73 HOH HOH . E 5 HOH A 74 574 60 HOH HOH . E 5 HOH A 75 575 107 HOH HOH . E 5 HOH A 76 576 189 HOH HOH . E 5 HOH A 77 577 6 HOH HOH . E 5 HOH A 78 578 20 HOH HOH . E 5 HOH A 79 579 196 HOH HOH . E 5 HOH A 80 580 102 HOH HOH . E 5 HOH A 81 581 3 HOH HOH . E 5 HOH A 82 582 200 HOH HOH . E 5 HOH A 83 583 112 HOH HOH . E 5 HOH A 84 584 208 HOH HOH . E 5 HOH A 85 585 64 HOH HOH . E 5 HOH A 86 586 91 HOH HOH . E 5 HOH A 87 587 167 HOH HOH . E 5 HOH A 88 588 19 HOH HOH . E 5 HOH A 89 589 162 HOH HOH . E 5 HOH A 90 590 28 HOH HOH . E 5 HOH A 91 591 157 HOH HOH . E 5 HOH A 92 592 89 HOH HOH . E 5 HOH A 93 593 138 HOH HOH . E 5 HOH A 94 594 35 HOH HOH . E 5 HOH A 95 595 74 HOH HOH . E 5 HOH A 96 596 21 HOH HOH . E 5 HOH A 97 597 67 HOH HOH . E 5 HOH A 98 598 8 HOH HOH . E 5 HOH A 99 599 69 HOH HOH . E 5 HOH A 100 600 184 HOH HOH . E 5 HOH A 101 601 38 HOH HOH . E 5 HOH A 102 602 83 HOH HOH . E 5 HOH A 103 603 136 HOH HOH . E 5 HOH A 104 604 126 HOH HOH . E 5 HOH A 105 605 179 HOH HOH . E 5 HOH A 106 606 59 HOH HOH . E 5 HOH A 107 607 100 HOH HOH . E 5 HOH A 108 608 71 HOH HOH . E 5 HOH A 109 609 49 HOH HOH . E 5 HOH A 110 610 106 HOH HOH . E 5 HOH A 111 611 175 HOH HOH . E 5 HOH A 112 612 53 HOH HOH . E 5 HOH A 113 613 166 HOH HOH . E 5 HOH A 114 614 181 HOH HOH . E 5 HOH A 115 615 77 HOH HOH . E 5 HOH A 116 616 15 HOH HOH . E 5 HOH A 117 617 206 HOH HOH . E 5 HOH A 118 618 78 HOH HOH . E 5 HOH A 119 619 194 HOH HOH . E 5 HOH A 120 620 178 HOH HOH . E 5 HOH A 121 621 5 HOH HOH . E 5 HOH A 122 622 120 HOH HOH . E 5 HOH A 123 623 32 HOH HOH . E 5 HOH A 124 624 158 HOH HOH . E 5 HOH A 125 625 153 HOH HOH . E 5 HOH A 126 626 87 HOH HOH . E 5 HOH A 127 627 27 HOH HOH . E 5 HOH A 128 628 88 HOH HOH . E 5 HOH A 129 629 203 HOH HOH . E 5 HOH A 130 630 104 HOH HOH . E 5 HOH A 131 631 18 HOH HOH . E 5 HOH A 132 632 37 HOH HOH . E 5 HOH A 133 633 81 HOH HOH . E 5 HOH A 134 634 161 HOH HOH . E 5 HOH A 135 635 154 HOH HOH . E 5 HOH A 136 636 156 HOH HOH . E 5 HOH A 137 637 187 HOH HOH . E 5 HOH A 138 638 115 HOH HOH . E 5 HOH A 139 639 177 HOH HOH . E 5 HOH A 140 640 14 HOH HOH . E 5 HOH A 141 641 16 HOH HOH . E 5 HOH A 142 642 39 HOH HOH . E 5 HOH A 143 643 75 HOH HOH . E 5 HOH A 144 644 41 HOH HOH . E 5 HOH A 145 645 11 HOH HOH . E 5 HOH A 146 646 50 HOH HOH . E 5 HOH A 147 647 149 HOH HOH . E 5 HOH A 148 648 135 HOH HOH . E 5 HOH A 149 649 133 HOH HOH . E 5 HOH A 150 650 176 HOH HOH . E 5 HOH A 151 651 209 HOH HOH . E 5 HOH A 152 652 197 HOH HOH . E 5 HOH A 153 653 101 HOH HOH . E 5 HOH A 154 654 93 HOH HOH . E 5 HOH A 155 655 97 HOH HOH . E 5 HOH A 156 656 103 HOH HOH . E 5 HOH A 157 657 168 HOH HOH . E 5 HOH A 158 658 164 HOH HOH . E 5 HOH A 159 659 144 HOH HOH . E 5 HOH A 160 660 57 HOH HOH . E 5 HOH A 161 661 65 HOH HOH . E 5 HOH A 162 662 193 HOH HOH . E 5 HOH A 163 663 145 HOH HOH . E 5 HOH A 164 664 123 HOH HOH . E 5 HOH A 165 665 180 HOH HOH . F 5 HOH D 1 201 143 HOH HOH . F 5 HOH D 2 202 155 HOH HOH . F 5 HOH D 3 203 26 HOH HOH . F 5 HOH D 4 204 205 HOH HOH . F 5 HOH D 5 205 31 HOH HOH . F 5 HOH D 6 206 146 HOH HOH . F 5 HOH D 7 207 186 HOH HOH . F 5 HOH D 8 208 117 HOH HOH . F 5 HOH D 9 209 183 HOH HOH . F 5 HOH D 10 210 165 HOH HOH . F 5 HOH D 11 211 173 HOH HOH . F 5 HOH D 12 212 195 HOH HOH . F 5 HOH D 13 213 148 HOH HOH . F 5 HOH D 14 214 2 HOH HOH . F 5 HOH D 15 215 190 HOH HOH . F 5 HOH D 16 216 46 HOH HOH . F 5 HOH D 17 217 147 HOH HOH . F 5 HOH D 18 218 130 HOH HOH . F 5 HOH D 19 219 105 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 . . . D 4 4.694 -34.347 30.88 1 28.94 ? C1 RIP 101 D 1 HETATM 2 C C2 RIP . . . D 4 5.457 -35.118 31.944 1 26.11 ? C2 RIP 101 D 1 HETATM 3 C C3 RIP . . . D 4 5.064 -34.652 33.344 1 26.22 ? C3 RIP 101 D 1 HETATM 4 C C4 RIP . . . D 4 3.558 -34.629 33.568 1 33.55 ? C4 RIP 101 D 1 HETATM 5 C C5 RIP . . . D 4 2.892 -33.925 32.398 1 21.1 ? C5 RIP 101 D 1 HETATM 6 O O2 RIP . . . D 4 5.195 -36.501 31.751 1 26.13 ? O2 RIP 101 D 1 HETATM 7 O O3 RIP . . . D 4 5.705 -35.469 34.323 1 28.8 ? O3 RIP 101 D 1 HETATM 8 O O4 RIP . . . D 4 3.015 -35.951 33.686 1 25.97 ? O4 RIP 101 D 1 HETATM 9 O O5 RIP . . . D 4 3.306 -34.5 31.157 1 25.92 ? O5 RIP 101 D 1 HETATM 10 H H1 RIP . . . D 4 4.931 -34.71 29.881 1 34.73 ? H1 RIP 101 D 1 HETATM 11 H H2 RIP . . . D 4 6.525 -34.94 31.824 1 31.33 ? H2 RIP 101 D 1 HETATM 12 H H3 RIP . . . D 4 5.431 -33.635 33.477 1 31.46 ? H3 RIP 101 D 1 HETATM 13 H H4 RIP . . . D 4 3.311 -34.165 34.522 1 40.26 ? H4 RIP 101 D 1 HETATM 14 H H51 RIP . . . D 4 3.207 -32.887 32.303 1 25.32 ? H51 RIP 101 D 1 HETATM 15 H H52 RIP . . . D 4 1.806 -33.927 32.479 1 25.32 ? H52 RIP 101 D 1 HETATM 16 H HO2 RIP . . . D 4 5.966 -36.872 31.246 1 31.35 ? HO2 RIP 101 D 1 HETATM 17 H HO3 RIP . . . D 4 6.127 -34.858 34.983 1 34.56 ? HO3 RIP 101 D 1 HETATM 18 H HO4 RIP . . . D 4 2.782 -36.287 32.781 1 31.16 ? HO4 RIP 101 D 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 18 #