data_4YPF # _model_server_result.job_id wk99-CNiQ-LENCGqG3fu5g _model_server_result.datetime_utc '2024-10-14 23:21:35' _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 4ypf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":508}' # _entry.id 4YPF # _exptl.entry_id 4YPF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 78.133 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIMETHYL SULFOXIDE' _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 92.55 _cell.angle_gamma 90 _cell.entry_id 4YPF _cell.length_a 64.665 _cell.length_b 119.14 _cell.length_c 66.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 2 1' # _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,I,J _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' 2_756 -x+2,y,-z+1 -1 0 0 0 1 0 0 0 -1 126.389131 0 66.034546 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H N N ? 6 I N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id F _struct_conn.ptnr1_label_atom_id S _struct_conn.ptnr1_label_comp_id SO4 _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id SO4 _struct_conn.ptnr1_auth_seq_id 505 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id F _struct_conn.ptnr2_label_atom_id S _struct_conn.ptnr2_label_comp_id SO4 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id SO4 _struct_conn.ptnr2_auth_seq_id 505 _struct_conn.ptnr2_symmetry 2_756 _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 1.927 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C2 H6 O S' _chem_comp.formula_weight 78.133 _chem_comp.id DMS _chem_comp.mon_nstd_flag . _chem_comp.name 'DIMETHYL SULFOXIDE' _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 S O DMS doub 103 n n S C1 DMS sing 104 n n S C2 DMS sing 105 n n C1 H11 DMS sing 106 n n C1 H12 DMS sing 107 n n C1 H13 DMS sing 108 n n C2 H21 DMS sing 109 n n C2 H22 DMS sing 110 n n C2 H23 DMS sing 111 n n # _atom_sites.entry_id 4YPF _atom_sites.fract_transf_matrix[1][1] 0.015464 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00069 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008393 _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] 0.015144 _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 B 2 HIS A 1 501 501 HIS HIS . C 3 4FS A 1 502 1 4FS 084 . D 4 EDO A 1 503 1 EDO EDO . E 5 SO4 A 1 504 2 SO4 SO4 . F 5 SO4 A 1 505 3 SO4 SO4 . G 5 SO4 A 1 506 4 SO4 SO4 . H 6 DMS A 1 507 5 DMS DMS . I 6 DMS A 1 508 6 DMS DMS . J 7 HOH A 1 601 208 HOH HOH . J 7 HOH A 2 602 152 HOH HOH . J 7 HOH A 3 603 202 HOH HOH . J 7 HOH A 4 604 206 HOH HOH . J 7 HOH A 5 605 8 HOH HOH . J 7 HOH A 6 606 88 HOH HOH . J 7 HOH A 7 607 47 HOH HOH . J 7 HOH A 8 608 59 HOH HOH . J 7 HOH A 9 609 209 HOH HOH . J 7 HOH A 10 610 16 HOH HOH . J 7 HOH A 11 611 75 HOH HOH . J 7 HOH A 12 612 102 HOH HOH . J 7 HOH A 13 613 156 HOH HOH . J 7 HOH A 14 614 33 HOH HOH . J 7 HOH A 15 615 5 HOH HOH . J 7 HOH A 16 616 22 HOH HOH . J 7 HOH A 17 617 51 HOH HOH . J 7 HOH A 18 618 82 HOH HOH . J 7 HOH A 19 619 142 HOH HOH . J 7 HOH A 20 620 38 HOH HOH . J 7 HOH A 21 621 24 HOH HOH . J 7 HOH A 22 622 45 HOH HOH . J 7 HOH A 23 623 56 HOH HOH . J 7 HOH A 24 624 144 HOH HOH . J 7 HOH A 25 625 19 HOH HOH . J 7 HOH A 26 626 139 HOH HOH . J 7 HOH A 27 627 48 HOH HOH . J 7 HOH A 28 628 21 HOH HOH . J 7 HOH A 29 629 201 HOH HOH . J 7 HOH A 30 630 141 HOH HOH . J 7 HOH A 31 631 222 HOH HOH . J 7 HOH A 32 632 15 HOH HOH . J 7 HOH A 33 633 173 HOH HOH . J 7 HOH A 34 634 198 HOH HOH . J 7 HOH A 35 635 196 HOH HOH . J 7 HOH A 36 636 200 HOH HOH . J 7 HOH A 37 637 20 HOH HOH . J 7 HOH A 38 638 6 HOH HOH . J 7 HOH A 39 639 204 HOH HOH . J 7 HOH A 40 640 34 HOH HOH . J 7 HOH A 41 641 106 HOH HOH . J 7 HOH A 42 642 4 HOH HOH . J 7 HOH A 43 643 39 HOH HOH . J 7 HOH A 44 644 17 HOH HOH . J 7 HOH A 45 645 223 HOH HOH . J 7 HOH A 46 646 13 HOH HOH . J 7 HOH A 47 647 60 HOH HOH . J 7 HOH A 48 648 203 HOH HOH . J 7 HOH A 49 649 97 HOH HOH . J 7 HOH A 50 650 44 HOH HOH . J 7 HOH A 51 651 103 HOH HOH . J 7 HOH A 52 652 205 HOH HOH . J 7 HOH A 53 653 14 HOH HOH . J 7 HOH A 54 654 46 HOH HOH . J 7 HOH A 55 655 76 HOH HOH . J 7 HOH A 56 656 194 HOH HOH . J 7 HOH A 57 657 72 HOH HOH . J 7 HOH A 58 658 77 HOH HOH . J 7 HOH A 59 659 68 HOH HOH . J 7 HOH A 60 660 55 HOH HOH . J 7 HOH A 61 661 81 HOH HOH . J 7 HOH A 62 662 1 HOH HOH . J 7 HOH A 63 663 65 HOH HOH . J 7 HOH A 64 664 118 HOH HOH . J 7 HOH A 65 665 91 HOH HOH . J 7 HOH A 66 666 2 HOH HOH . J 7 HOH A 67 667 67 HOH HOH . J 7 HOH A 68 668 138 HOH HOH . J 7 HOH A 69 669 18 HOH HOH . J 7 HOH A 70 670 35 HOH HOH . J 7 HOH A 71 671 224 HOH HOH . J 7 HOH A 72 672 62 HOH HOH . J 7 HOH A 73 673 169 HOH HOH . J 7 HOH A 74 674 184 HOH HOH . J 7 HOH A 75 675 23 HOH HOH . J 7 HOH A 76 676 218 HOH HOH . J 7 HOH A 77 677 7 HOH HOH . J 7 HOH A 78 678 215 HOH HOH . J 7 HOH A 79 679 185 HOH HOH . J 7 HOH A 80 680 216 HOH HOH . J 7 HOH A 81 681 214 HOH HOH . J 7 HOH A 82 682 210 HOH HOH . J 7 HOH A 83 683 221 HOH HOH . J 7 HOH A 84 684 146 HOH HOH . J 7 HOH A 85 685 213 HOH HOH . J 7 HOH A 86 686 26 HOH HOH . J 7 HOH A 87 687 30 HOH HOH . J 7 HOH A 88 688 131 HOH HOH . J 7 HOH A 89 689 220 HOH HOH . J 7 HOH A 90 690 211 HOH HOH . J 7 HOH A 91 691 212 HOH HOH . J 7 HOH A 92 692 128 HOH HOH . J 7 HOH A 93 693 143 HOH HOH . J 7 HOH A 94 694 217 HOH HOH . J 7 HOH A 95 695 219 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 S S DMS . . . I 6 82.229 14.85 24.092 1 73.19 ? S DMS 508 A 1 HETATM 2 O O DMS . . . I 6 82.603 14.016 25.256 1 72.13 ? O DMS 508 A 1 HETATM 3 C C1 DMS . . . I 6 82.09 13.856 22.71 1 71.38 ? C1 DMS 508 A 1 HETATM 4 C C2 DMS . . . I 6 80.633 15.409 24.286 1 68.64 ? C2 DMS 508 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 52 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 439 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 4 #