data_8G2G # _model_server_result.job_id YoINZoyRSMRU8yRO_D1-_A _model_server_result.datetime_utc '2025-07-15 17:04:25' _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 8g2g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 8G2G # _exptl.entry_id 8G2G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 459.522 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine" _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 90 _cell.angle_gamma 90 _cell.entry_id 8G2G _cell.length_a 95.808 _cell.length_b 99.863 _cell.length_c 170.314 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8G2G _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,G 1 1,2 B,F,H 2 1,3 # 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 85.157 3 'crystal symmetry operation' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 99.863 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N N # _chem_comp.formula 'C20 H25 N7 O4 S' _chem_comp.formula_weight 459.522 _chem_comp.id YVU _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine" _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 N C YVU sing 380 n n N3 C3 YVU sing 381 n y N3 C4 YVU doub 382 n y C C3 YVU sing 383 n y C N1 YVU doub 384 n y C3 C2 YVU doub 385 n y C4 N4 YVU sing 386 n y N1 C1 YVU sing 387 n y C2 N4 YVU sing 388 n y C2 N2 YVU sing 389 n y N4 C5 YVU sing 390 n n C7 S YVU sing 391 n n C7 C6 YVU sing 392 n n C1 N2 YVU doub 393 n y O C5 YVU sing 394 n n O C6 YVU sing 395 n n C16 C15 YVU doub 396 n y C16 C17 YVU sing 397 n y S C8 YVU sing 398 n n C5 C19 YVU sing 399 n n C6 C18 YVU sing 400 n n C15 C14 YVU sing 401 n y C8 C9 YVU sing 402 n n C19 C18 YVU sing 403 n n C19 O3 YVU sing 404 n n C17 C12 YVU doub 405 n y C18 O2 YVU sing 406 n n C14 C13 YVU doub 407 n y C9 N5 YVU sing 408 n n N5 C10 YVU sing 409 n n C12 C13 YVU sing 410 n y C12 C11 YVU sing 411 n n C10 N6 YVU sing 412 n n C10 O1 YVU doub 413 n n N6 C11 YVU sing 414 n n C7 H1 YVU sing 415 n n C7 H2 YVU sing 416 n n C8 H3 YVU sing 417 n n C8 H4 YVU sing 418 n n C9 H5 YVU sing 419 n n C9 H6 YVU sing 420 n n C1 H7 YVU sing 421 n n C5 H8 YVU sing 422 n n C6 H9 YVU sing 423 n n C4 H10 YVU sing 424 n n O3 H11 YVU sing 425 n n N6 H12 YVU sing 426 n n C11 H13 YVU sing 427 n n C11 H14 YVU sing 428 n n C17 H15 YVU sing 429 n n C16 H16 YVU sing 430 n n C15 H17 YVU sing 431 n n C14 H18 YVU sing 432 n n C13 H19 YVU sing 433 n n N5 H20 YVU sing 434 n n C18 H21 YVU sing 435 n n O2 H22 YVU sing 436 n n C19 H23 YVU sing 437 n n N H24 YVU sing 438 n n N H25 YVU sing 439 n n # _atom_sites.entry_id 8G2G _atom_sites.fract_transf_matrix[1][1] 0.010438 _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] 0.010014 _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] 0.005872 _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 2 YVU A 1 601 601 YVU XXX . D 3 SO4 A 1 602 1 SO4 SO4 . E 3 SO4 A 1 603 2 SO4 SO4 . F 2 YVU B 1 601 601 YVU XXX . G 4 HOH A 1 701 154 HOH HOH . G 4 HOH A 2 702 153 HOH HOH . G 4 HOH A 3 703 150 HOH HOH . G 4 HOH A 4 704 54 HOH HOH . G 4 HOH A 5 705 43 HOH HOH . G 4 HOH A 6 706 106 HOH HOH . G 4 HOH A 7 707 65 HOH HOH . G 4 HOH A 8 708 112 HOH HOH . G 4 HOH A 9 709 89 HOH HOH . G 4 HOH A 10 710 93 HOH HOH . G 4 HOH A 11 711 46 HOH HOH . G 4 HOH A 12 712 118 HOH HOH . G 4 HOH A 13 713 113 HOH HOH . G 4 HOH A 14 714 11 HOH HOH . G 4 HOH A 15 715 18 HOH HOH . G 4 HOH A 16 716 36 HOH HOH . G 4 HOH A 17 717 85 HOH HOH . G 4 HOH A 18 718 90 HOH HOH . G 4 HOH A 19 719 111 HOH HOH . G 4 HOH A 20 720 100 HOH HOH . G 4 HOH A 21 721 162 HOH HOH . G 4 HOH A 22 722 17 HOH HOH . G 4 HOH A 23 723 161 HOH HOH . G 4 HOH A 24 724 32 HOH HOH . G 4 HOH A 25 725 98 HOH HOH . G 4 HOH A 26 726 42 HOH HOH . G 4 HOH A 27 727 119 HOH HOH . G 4 HOH A 28 728 116 HOH HOH . G 4 HOH A 29 729 95 HOH HOH . G 4 HOH A 30 730 53 HOH HOH . G 4 HOH A 31 731 144 HOH HOH . G 4 HOH A 32 732 148 HOH HOH . G 4 HOH A 33 733 109 HOH HOH . G 4 HOH A 34 734 94 HOH HOH . G 4 HOH A 35 735 88 HOH HOH . G 4 HOH A 36 736 80 HOH HOH . G 4 HOH A 37 737 115 HOH HOH . G 4 HOH A 38 738 20 HOH HOH . G 4 HOH A 39 739 97 HOH HOH . G 4 HOH A 40 740 108 HOH HOH . G 4 HOH A 41 741 72 HOH HOH . G 4 HOH A 42 742 70 HOH HOH . G 4 HOH A 43 743 56 HOH HOH . G 4 HOH A 44 744 66 HOH HOH . G 4 HOH A 45 745 81 HOH HOH . G 4 HOH A 46 746 91 HOH HOH . G 4 HOH A 47 747 37 HOH HOH . G 4 HOH A 48 748 8 HOH HOH . G 4 HOH A 49 749 69 HOH HOH . G 4 HOH A 50 750 96 HOH HOH . G 4 HOH A 51 751 2 HOH HOH . G 4 HOH A 52 752 79 HOH HOH . G 4 HOH A 53 753 3 HOH HOH . G 4 HOH A 54 754 13 HOH HOH . G 4 HOH A 55 755 74 HOH HOH . G 4 HOH A 56 756 33 HOH HOH . G 4 HOH A 57 757 114 HOH HOH . G 4 HOH A 58 758 104 HOH HOH . G 4 HOH A 59 759 103 HOH HOH . G 4 HOH A 60 760 50 HOH HOH . G 4 HOH A 61 761 51 HOH HOH . G 4 HOH A 62 762 107 HOH HOH . G 4 HOH A 63 763 28 HOH HOH . G 4 HOH A 64 764 92 HOH HOH . G 4 HOH A 65 765 155 HOH HOH . G 4 HOH A 66 766 82 HOH HOH . G 4 HOH A 67 767 57 HOH HOH . G 4 HOH A 68 768 105 HOH HOH . G 4 HOH A 69 769 99 HOH HOH . G 4 HOH A 70 770 86 HOH HOH . G 4 HOH A 71 771 61 HOH HOH . G 4 HOH A 72 772 40 HOH HOH . G 4 HOH A 73 773 62 HOH HOH . G 4 HOH A 74 774 76 HOH HOH . G 4 HOH A 75 775 12 HOH HOH . G 4 HOH A 76 776 4 HOH HOH . G 4 HOH A 77 777 14 HOH HOH . G 4 HOH A 78 778 102 HOH HOH . G 4 HOH A 79 779 27 HOH HOH . G 4 HOH A 80 780 71 HOH HOH . G 4 HOH A 81 781 22 HOH HOH . G 4 HOH A 82 782 84 HOH HOH . G 4 HOH A 83 783 101 HOH HOH . G 4 HOH A 84 784 10 HOH HOH . G 4 HOH A 85 785 83 HOH HOH . G 4 HOH A 86 786 151 HOH HOH . G 4 HOH A 87 787 149 HOH HOH . H 4 HOH B 1 701 47 HOH HOH . H 4 HOH B 2 702 123 HOH HOH . H 4 HOH B 3 703 128 HOH HOH . H 4 HOH B 4 704 120 HOH HOH . H 4 HOH B 5 705 140 HOH HOH . H 4 HOH B 6 706 16 HOH HOH . H 4 HOH B 7 707 122 HOH HOH . H 4 HOH B 8 708 126 HOH HOH . H 4 HOH B 9 709 25 HOH HOH . H 4 HOH B 10 710 48 HOH HOH . H 4 HOH B 11 711 31 HOH HOH . H 4 HOH B 12 712 135 HOH HOH . H 4 HOH B 13 713 49 HOH HOH . H 4 HOH B 14 714 117 HOH HOH . H 4 HOH B 15 715 124 HOH HOH . H 4 HOH B 16 716 131 HOH HOH . H 4 HOH B 17 717 34 HOH HOH . H 4 HOH B 18 718 75 HOH HOH . H 4 HOH B 19 719 29 HOH HOH . H 4 HOH B 20 720 15 HOH HOH . H 4 HOH B 21 721 164 HOH HOH . H 4 HOH B 22 722 67 HOH HOH . H 4 HOH B 23 723 87 HOH HOH . H 4 HOH B 24 724 166 HOH HOH . H 4 HOH B 25 725 68 HOH HOH . H 4 HOH B 26 726 147 HOH HOH . H 4 HOH B 27 727 141 HOH HOH . H 4 HOH B 28 728 139 HOH HOH . H 4 HOH B 29 729 52 HOH HOH . H 4 HOH B 30 730 78 HOH HOH . H 4 HOH B 31 731 38 HOH HOH . H 4 HOH B 32 732 133 HOH HOH . H 4 HOH B 33 733 134 HOH HOH . H 4 HOH B 34 734 146 HOH HOH . H 4 HOH B 35 735 23 HOH HOH . H 4 HOH B 36 736 77 HOH HOH . H 4 HOH B 37 737 21 HOH HOH . H 4 HOH B 38 738 35 HOH HOH . H 4 HOH B 39 739 152 HOH HOH . H 4 HOH B 40 740 59 HOH HOH . H 4 HOH B 41 741 6 HOH HOH . H 4 HOH B 42 742 9 HOH HOH . H 4 HOH B 43 743 24 HOH HOH . H 4 HOH B 44 744 132 HOH HOH . H 4 HOH B 45 745 44 HOH HOH . H 4 HOH B 46 746 127 HOH HOH . H 4 HOH B 47 747 156 HOH HOH . H 4 HOH B 48 748 73 HOH HOH . H 4 HOH B 49 749 168 HOH HOH . H 4 HOH B 50 750 58 HOH HOH . H 4 HOH B 51 751 39 HOH HOH . H 4 HOH B 52 752 19 HOH HOH . H 4 HOH B 53 753 142 HOH HOH . H 4 HOH B 54 754 30 HOH HOH . H 4 HOH B 55 755 121 HOH HOH . H 4 HOH B 56 756 45 HOH HOH . H 4 HOH B 57 757 158 HOH HOH . H 4 HOH B 58 758 159 HOH HOH . H 4 HOH B 59 759 138 HOH HOH . H 4 HOH B 60 760 5 HOH HOH . H 4 HOH B 61 761 63 HOH HOH . H 4 HOH B 62 762 163 HOH HOH . H 4 HOH B 63 763 64 HOH HOH . H 4 HOH B 64 764 60 HOH HOH . H 4 HOH B 65 765 165 HOH HOH . H 4 HOH B 66 766 125 HOH HOH . H 4 HOH B 67 767 1 HOH HOH . H 4 HOH B 68 768 41 HOH HOH . H 4 HOH B 69 769 143 HOH HOH . H 4 HOH B 70 770 160 HOH HOH . H 4 HOH B 71 771 136 HOH HOH . H 4 HOH B 72 772 129 HOH HOH . H 4 HOH B 73 773 137 HOH HOH . H 4 HOH B 74 774 167 HOH HOH . H 4 HOH B 75 775 145 HOH HOH . H 4 HOH B 76 776 157 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 N N1 YVU . . . F 2 -17.8 32.027 3.373 1 41.7 ? N1 YVU 601 B 1 HETATM 2 C C7 YVU . . . F 2 -10.05 34.449 2.718 1 34.81 ? C7 YVU 601 B 1 HETATM 3 C C8 YVU . . . F 2 -7.775 33.102 1.744 1 36.35 ? C8 YVU 601 B 1 HETATM 4 N N2 YVU . . . F 2 -16.014 32.426 1.814 1 42.08 ? N2 YVU 601 B 1 HETATM 5 C C9 YVU . . . F 2 -7.902 32.647 0.302 1 36.39 ? C9 YVU 601 B 1 HETATM 6 O O1 YVU . . . F 2 -5.434 31.706 -0.572 1 30.54 ? O1 YVU 601 B 1 HETATM 7 C C1 YVU . . . F 2 -17.117 31.815 2.248 1 36.67 ? C1 YVU 601 B 1 HETATM 8 C C5 YVU . . . F 2 -13.352 33.974 1.673 1 39.78 ? C5 YVU 601 B 1 HETATM 9 C C6 YVU . . . F 2 -11.027 33.956 1.663 1 37.9 ? C6 YVU 601 B 1 HETATM 10 N N3 YVU . . . F 2 -15.43 34.605 4.591 1 41.26 ? N3 YVU 601 B 1 HETATM 11 C C4 YVU . . . F 2 -14.418 34.829 3.794 1 40.86 ? C4 YVU 601 B 1 HETATM 12 C C3 YVU . . . F 2 -16.182 33.661 3.908 1 42.23 ? C3 YVU 601 B 1 HETATM 13 O O3 YVU . . . F 2 -13.683 35.549 -0.18 1 37.32 ? O3 YVU 601 B 1 HETATM 14 C C2 YVU . . . F 2 -15.587 33.339 2.7 1 44.62 ? C2 YVU 601 B 1 HETATM 15 N N4 YVU . . . F 2 -14.437 34.089 2.641 1 43.67 ? N4 YVU 601 B 1 HETATM 16 C C10 YVU . . . F 2 -6.31 30.883 -0.277 1 33.48 ? C10 YVU 601 B 1 HETATM 17 N N6 YVU . . . F 2 -6.096 29.547 -0.331 1 32.84 ? N6 YVU 601 B 1 HETATM 18 C C11 YVU . . . F 2 -4.829 29.028 -0.821 1 30.67 ? C11 YVU 601 B 1 HETATM 19 C C12 YVU . . . F 2 -3.707 29.048 0.184 1 31.32 ? C12 YVU 601 B 1 HETATM 20 C C17 YVU . . . F 2 -3.956 29.261 1.535 1 30.17 ? C17 YVU 601 B 1 HETATM 21 C C16 YVU . . . F 2 -2.929 29.19 2.463 1 28.71 ? C16 YVU 601 B 1 HETATM 22 C C15 YVU . . . F 2 -1.649 28.899 2.057 1 30.44 ? C15 YVU 601 B 1 HETATM 23 C C14 YVU . . . F 2 -1.393 28.668 0.721 1 30.28 ? C14 YVU 601 B 1 HETATM 24 C C13 YVU . . . F 2 -2.405 28.767 -0.214 1 28.21 ? C13 YVU 601 B 1 HETATM 25 N N5 YVU . . . F 2 -7.525 31.247 0.164 1 34.92 ? N5 YVU 601 B 1 HETATM 26 S S YVU . . . F 2 -8.417 34.778 2 1 37.74 ? S YVU 601 B 1 HETATM 27 O O YVU . . . F 2 -12.207 33.524 2.369 1 37.55 ? O YVU 601 B 1 HETATM 28 C C18 YVU . . . F 2 -11.49 35.001 0.633 1 38.69 ? C18 YVU 601 B 1 HETATM 29 O O2 YVU . . . F 2 -11.413 34.603 -0.734 1 37.98 ? O2 YVU 601 B 1 HETATM 30 C C19 YVU . . . F 2 -12.95 35.276 1.011 1 39.01 ? C19 YVU 601 B 1 HETATM 31 C C YVU . . . F 2 -17.361 32.971 4.24 1 44.74 ? C YVU 601 B 1 HETATM 32 N N YVU . . . F 2 -18.064 33.201 5.357 1 41.14 ? N YVU 601 B 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #