data_8G2G
#
_model_server_result.job_id            ViySn7ZeFyFps5x9-Lu1ng 
_model_server_result.datetime_utc      '2025-07-13 22:53:07' 
_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":"C","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 . . . C 2 18.778 19.658 38.055 1 35.68 ? N1 YVU 601 A 1 
HETATM 2 C C7 YVU . . . C 2 16.01 12.033 39.098 1 33.16 ? C7 YVU 601 A 1 
HETATM 3 C C8 YVU . . . C 2 17.198 9.732 40.198 1 32.08 ? C8 YVU 601 A 1 
HETATM 4 N N2 YVU . . . C 2 18.32 17.935 39.679 1 33.72 ? N2 YVU 601 A 1 
HETATM 5 C C9 YVU . . . C 2 17.702 9.955 41.613 1 32.9 ? C9 YVU 601 A 1 
HETATM 6 O O1 YVU . . . C 2 18.485 7.417 42.614 1 29.77 ? O1 YVU 601 A 1 
HETATM 7 C C1 YVU . . . C 2 18.95 19.018 39.215 1 34.99 ? C1 YVU 601 A 1 
HETATM 8 C C5 YVU . . . C 2 16.657 15.325 39.921 1 33.73 ? C5 YVU 601 A 1 
HETATM 9 C C6 YVU . . . C 2 16.582 13.016 40.101 1 31.34 ? C6 YVU 601 A 1 
HETATM 10 N N3 YVU . . . C 2 16.15 17.299 36.908 1 32.58 ? N3 YVU 601 A 1 
HETATM 11 C C4 YVU . . . C 2 15.878 16.332 37.75 1 32.84 ? C4 YVU 601 A 1 
HETATM 12 C C3 YVU . . . C 2 17.124 18.041 37.56 1 34.07 ? C3 YVU 601 A 1 
HETATM 13 O O3 YVU . . . C 2 14.974 15.909 41.64 1 33.59 ? O3 YVU 601 A 1 
HETATM 14 C C2 YVU . . . C 2 17.424 17.48 38.793 1 33.89 ? C2 YVU 601 A 1 
HETATM 15 N N4 YVU . . . C 2 16.626 16.363 38.899 1 33.5 ? N4 YVU 601 A 1 
HETATM 16 C C10 YVU . . . C 2 19.343 8.228 42.286 1 29.74 ? C10 YVU 601 A 1 
HETATM 17 N N6 YVU . . . C 2 20.653 7.93 42.375 1 30.76 ? N6 YVU 601 A 1 
HETATM 18 C C11 YVU . . . C 2 21.072 6.647 42.912 1 28.67 ? C11 YVU 601 A 1 
HETATM 19 C C12 YVU . . . C 2 20.993 5.486 41.954 1 29.64 ? C12 YVU 601 A 1 
HETATM 20 C C17 YVU . . . C 2 20.83 5.686 40.586 1 30.68 ? C17 YVU 601 A 1 
HETATM 21 C C16 YVU . . . C 2 20.901 4.619 39.704 1 31.46 ? C16 YVU 601 A 1 
HETATM 22 C C15 YVU . . . C 2 21.126 3.341 40.175 1 30.95 ? C15 YVU 601 A 1 
HETATM 23 C C14 YVU . . . C 2 21.286 3.132 41.532 1 30.26 ? C14 YVU 601 A 1 
HETATM 24 C C13 YVU . . . C 2 21.197 4.193 42.416 1 30.96 ? C13 YVU 601 A 1 
HETATM 25 N N5 YVU . . . C 2 19.058 9.454 41.795 1 32.34 ? N5 YVU 601 A 1 
HETATM 26 S S YVU . . . C 2 15.573 10.481 39.874 1 32.76 ? S YVU 601 A 1 
HETATM 27 O O YVU . . . C 2 17.035 14.119 39.29 1 34.13 ? O YVU 601 A 1 
HETATM 28 C C18 YVU . . . C 2 15.551 13.581 41.086 1 32.38 ? C18 YVU 601 A 1 
HETATM 29 O O2 YVU . . . C 2 15.988 13.524 42.441 1 32.38 ? O2 YVU 601 A 1 
HETATM 30 C C19 YVU . . . C 2 15.317 15.016 40.583 1 33.94 ? C19 YVU 601 A 1 
HETATM 31 C C YVU . . . C 2 17.836 19.206 37.199 1 35.52 ? C YVU 601 A 1 
HETATM 32 N N YVU . . . C 2 17.577 19.93 36.108 1 32.08 ? N YVU 601 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           32 
#