data_6EMA # _model_server_result.job_id Rzik8UItr0utZGCeOmxFSQ _model_server_result.datetime_utc '2024-10-13 02:26:41' _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 6ema # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":101}' # _entry.id 6EMA # _exptl.entry_id 6EMA _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 6EMA _cell.length_a 68.86 _cell.length_b 73.433 _cell.length_c 76.94 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EMA _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 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 PHE 141 A PHE 138 1_555 A N SEP 142 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C SEP 142 A SEP 139 1_555 A N GLU 143 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C TRP 199 A TRP 196 1_555 A N TPO 200 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C TPO 200 A TPO 197 1_555 A N LEU 201 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C VAL 340 A VAL 337 1_555 A N SEP 341 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C SEP 341 A SEP 338 1_555 A N ILE 342 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? # _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 6EMA _atom_sites.fract_transf_matrix[1][1] 0.014522 _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] 0.013618 _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] 0.012997 _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 ATP A 1 401 1 ATP ATP . D 4 RIP C 1 101 1 RIP RIB . E 5 HOH A 1 501 111 HOH HOH . E 5 HOH A 2 502 83 HOH HOH . E 5 HOH A 3 503 21 HOH HOH . E 5 HOH A 4 504 91 HOH HOH . E 5 HOH A 5 505 47 HOH HOH . E 5 HOH A 6 506 75 HOH HOH . E 5 HOH A 7 507 3 HOH HOH . E 5 HOH A 8 508 46 HOH HOH . E 5 HOH A 9 509 76 HOH HOH . E 5 HOH A 10 510 54 HOH HOH . E 5 HOH A 11 511 99 HOH HOH . E 5 HOH A 12 512 26 HOH HOH . E 5 HOH A 13 513 50 HOH HOH . E 5 HOH A 14 514 14 HOH HOH . E 5 HOH A 15 515 53 HOH HOH . E 5 HOH A 16 516 52 HOH HOH . E 5 HOH A 17 517 42 HOH HOH . E 5 HOH A 18 518 104 HOH HOH . E 5 HOH A 19 519 45 HOH HOH . E 5 HOH A 20 520 22 HOH HOH . E 5 HOH A 21 521 17 HOH HOH . E 5 HOH A 22 522 72 HOH HOH . E 5 HOH A 23 523 126 HOH HOH . E 5 HOH A 24 524 8 HOH HOH . E 5 HOH A 25 525 19 HOH HOH . E 5 HOH A 26 526 66 HOH HOH . E 5 HOH A 27 527 43 HOH HOH . E 5 HOH A 28 528 57 HOH HOH . E 5 HOH A 29 529 5 HOH HOH . E 5 HOH A 30 530 36 HOH HOH . E 5 HOH A 31 531 103 HOH HOH . E 5 HOH A 32 532 69 HOH HOH . E 5 HOH A 33 533 16 HOH HOH . E 5 HOH A 34 534 4 HOH HOH . E 5 HOH A 35 535 95 HOH HOH . E 5 HOH A 36 536 6 HOH HOH . E 5 HOH A 37 537 35 HOH HOH . E 5 HOH A 38 538 118 HOH HOH . E 5 HOH A 39 539 41 HOH HOH . E 5 HOH A 40 540 25 HOH HOH . E 5 HOH A 41 541 62 HOH HOH . E 5 HOH A 42 542 28 HOH HOH . E 5 HOH A 43 543 2 HOH HOH . E 5 HOH A 44 544 78 HOH HOH . E 5 HOH A 45 545 20 HOH HOH . E 5 HOH A 46 546 7 HOH HOH . E 5 HOH A 47 547 15 HOH HOH . E 5 HOH A 48 548 9 HOH HOH . E 5 HOH A 49 549 127 HOH HOH . E 5 HOH A 50 550 80 HOH HOH . E 5 HOH A 51 551 56 HOH HOH . E 5 HOH A 52 552 31 HOH HOH . E 5 HOH A 53 553 39 HOH HOH . E 5 HOH A 54 554 12 HOH HOH . E 5 HOH A 55 555 82 HOH HOH . E 5 HOH A 56 556 27 HOH HOH . E 5 HOH A 57 557 60 HOH HOH . E 5 HOH A 58 558 88 HOH HOH . E 5 HOH A 59 559 10 HOH HOH . E 5 HOH A 60 560 125 HOH HOH . E 5 HOH A 61 561 74 HOH HOH . E 5 HOH A 62 562 40 HOH HOH . E 5 HOH A 63 563 79 HOH HOH . E 5 HOH A 64 564 65 HOH HOH . E 5 HOH A 65 565 110 HOH HOH . E 5 HOH A 66 566 61 HOH HOH . E 5 HOH A 67 567 92 HOH HOH . E 5 HOH A 68 568 32 HOH HOH . E 5 HOH A 69 569 23 HOH HOH . E 5 HOH A 70 570 37 HOH HOH . E 5 HOH A 71 571 116 HOH HOH . E 5 HOH A 72 572 51 HOH HOH . E 5 HOH A 73 573 67 HOH HOH . E 5 HOH A 74 574 114 HOH HOH . E 5 HOH A 75 575 63 HOH HOH . E 5 HOH A 76 576 87 HOH HOH . E 5 HOH A 77 577 107 HOH HOH . E 5 HOH A 78 578 101 HOH HOH . E 5 HOH A 79 579 59 HOH HOH . E 5 HOH A 80 580 100 HOH HOH . E 5 HOH A 81 581 24 HOH HOH . E 5 HOH A 82 582 77 HOH HOH . E 5 HOH A 83 583 29 HOH HOH . E 5 HOH A 84 584 97 HOH HOH . E 5 HOH A 85 585 73 HOH HOH . E 5 HOH A 86 586 113 HOH HOH . E 5 HOH A 87 587 44 HOH HOH . E 5 HOH A 88 588 13 HOH HOH . E 5 HOH A 89 589 38 HOH HOH . E 5 HOH A 90 590 18 HOH HOH . E 5 HOH A 91 591 86 HOH HOH . E 5 HOH A 92 592 115 HOH HOH . E 5 HOH A 93 593 11 HOH HOH . E 5 HOH A 94 594 34 HOH HOH . E 5 HOH A 95 595 96 HOH HOH . E 5 HOH A 96 596 98 HOH HOH . E 5 HOH A 97 597 122 HOH HOH . E 5 HOH A 98 598 58 HOH HOH . E 5 HOH A 99 599 123 HOH HOH . E 5 HOH A 100 600 81 HOH HOH . E 5 HOH A 101 601 71 HOH HOH . E 5 HOH A 102 602 128 HOH HOH . E 5 HOH A 103 603 85 HOH HOH . E 5 HOH A 104 604 109 HOH HOH . E 5 HOH A 105 605 93 HOH HOH . E 5 HOH A 106 606 94 HOH HOH . E 5 HOH A 107 607 106 HOH HOH . F 5 HOH C 1 201 48 HOH HOH . F 5 HOH C 2 202 120 HOH HOH . F 5 HOH C 3 203 1 HOH HOH . F 5 HOH C 4 204 105 HOH HOH . F 5 HOH C 5 205 108 HOH HOH . F 5 HOH C 6 206 70 HOH HOH . F 5 HOH C 7 207 64 HOH HOH . F 5 HOH C 8 208 121 HOH HOH . F 5 HOH C 9 209 30 HOH HOH . F 5 HOH C 10 210 124 HOH HOH . F 5 HOH C 11 211 102 HOH HOH . F 5 HOH C 12 212 119 HOH HOH . F 5 HOH C 13 213 33 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 -3.017 12.887 11.665 1 80.83 ? C1 RIP 101 C 1 HETATM 2 C C2 RIP . . . D 4 -3.034 11.449 11.22 1 71.49 ? C2 RIP 101 C 1 HETATM 3 C C3 RIP . . . D 4 -4.11 11.301 10.155 1 67.36 ? C3 RIP 101 C 1 HETATM 4 C C4 RIP . . . D 4 -3.833 12.237 8.987 1 72.44 ? C4 RIP 101 C 1 HETATM 5 C C5 RIP . . . D 4 -3.69 13.662 9.493 1 80.62 ? C5 RIP 101 C 1 HETATM 6 O O1 RIP . . . D 4 -4.291 13.038 12.182 1 67.84 ? O1 RIP 101 C 1 HETATM 7 O O2 RIP . . . D 4 -1.748 11.077 10.739 1 71.6 ? O2 RIP 101 C 1 HETATM 8 O O3 RIP . . . D 4 -4.185 9.953 9.708 1 75.76 ? O3 RIP 101 C 1 HETATM 9 O O4 RIP . . . D 4 -2.635 11.848 8.315 1 80.05 ? O4 RIP 101 C 1 HETATM 10 O O5 RIP . . . D 4 -2.737 13.752 10.563 1 92.32 ? O5 RIP 101 C 1 HETATM 11 H H1 RIP . . . D 4 -2.305 13.045 12.475 1 97 ? H1 RIP 101 C 1 HETATM 12 H H2 RIP . . . D 4 -3.303 10.809 12.059 1 85.78 ? H2 RIP 101 C 1 HETATM 13 H H3 RIP . . . D 4 -5.073 11.57 10.587 1 80.83 ? H3 RIP 101 C 1 HETATM 14 H H4 RIP . . . D 4 -4.6 12.146 8.22 1 86.93 ? H4 RIP 101 C 1 HETATM 15 H H51 RIP . . . D 4 -3.27 14.328 8.741 1 96.75 ? H51 RIP 101 C 1 HETATM 16 H H52 RIP . . . D 4 -4.645 14.087 9.798 1 96.75 ? H52 RIP 101 C 1 HETATM 17 H HO1 RIP . . . D 4 -4.889 13.43 11.494 1 81.41 ? HO1 RIP 101 C 1 HETATM 18 H HO2 RIP . . . D 4 -1.257 10.684 11.507 1 85.92 ? HO2 RIP 101 C 1 HETATM 19 H HO3 RIP . . . D 4 -4.996 9.554 10.119 1 90.91 ? HO3 RIP 101 C 1 HETATM 20 H HO4 RIP . . . D 4 -2.805 11.828 7.337 1 96.05 ? HO4 RIP 101 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #