data_5ISC # _model_server_result.job_id HVI2nVIBvv6YZibZo5xWTA _model_server_result.datetime_utc '2024-11-25 06:43:07' _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 5isc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 5ISC # _exptl.entry_id 5ISC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 502.32 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-{[(3S)-3-amino-3-carboxypropyl](3-bromo-2-oxopropyl)amino}-5'-deoxyadenosine" _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 5ISC _cell.length_a 79.123 _cell.length_b 101.043 _cell.length_c 211.349 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ISC _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 O N N # _chem_comp.formula 'C17 H24 Br N7 O6' _chem_comp.formula_weight 502.32 _chem_comp.id 6D0 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl](3-bromo-2-oxopropyl)amino}-5'-deoxyadenosine" _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 C14 N7 6D0 doub 1 n y C14 N6 6D0 sing 2 n y N7 C12 6D0 sing 3 n y N6 C13 6D0 doub 4 n y C12 N5 6D0 sing 5 n n C12 C11 6D0 doub 6 n y C13 C11 6D0 sing 7 n y C13 N3 6D0 sing 8 n y O3 C8 6D0 sing 9 n n O4 C9 6D0 sing 10 n n C11 N4 6D0 sing 11 n y C7 N3 6D0 sing 12 n n C7 C8 6D0 sing 13 n n C7 O2 6D0 sing 14 n n N3 C10 6D0 sing 15 n y C8 C9 6D0 sing 16 n n O2 C6 6D0 sing 17 n n C9 C6 6D0 sing 18 n n C2 C1 6D0 sing 19 n n C2 C3 6D0 sing 20 n n C2 N1 6D0 sing 21 n n N4 C10 6D0 doub 22 n y C6 C5 6D0 sing 23 n n C1 O1 6D0 doub 24 n n C1 O6 6D0 sing 25 n n C3 C4 6D0 sing 26 n n C5 N2 6D0 sing 27 n n C4 N2 6D0 sing 28 n n N2 C15 6D0 sing 29 n n C15 C16 6D0 sing 30 n n O5 C16 6D0 doub 31 n n C16 C17 6D0 sing 32 n n C17 BR1 6D0 sing 33 n n C2 H1 6D0 sing 34 n n N1 H2 6D0 sing 35 n n N1 H3 6D0 sing 36 n n C3 H5 6D0 sing 37 n n C3 H6 6D0 sing 38 n n C4 H7 6D0 sing 39 n n C4 H8 6D0 sing 40 n n C5 H10 6D0 sing 41 n n C5 H11 6D0 sing 42 n n C6 H12 6D0 sing 43 n n C7 H13 6D0 sing 44 n n C8 H14 6D0 sing 45 n n O3 H15 6D0 sing 46 n n C9 H16 6D0 sing 47 n n O4 H17 6D0 sing 48 n n C10 H18 6D0 sing 49 n n N5 H19 6D0 sing 50 n n N5 H20 6D0 sing 51 n n C14 H21 6D0 sing 52 n n C15 H22 6D0 sing 53 n n C15 H23 6D0 sing 54 n n C17 H24 6D0 sing 55 n n C17 H25 6D0 sing 56 n n O6 H26 6D0 sing 57 n n # _atom_sites.entry_id 5ISC _atom_sites.fract_transf_matrix[1][1] 0.012639 _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] 0.009897 _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] 0.004732 _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 E 2 SAO A 1 501 1 SAO SAH . F 3 EDO A 1 502 2 EDO EDO . G 3 EDO A 1 503 3 EDO EDO . H 3 EDO A 1 504 6 EDO EDO . I 4 6D0 B 1 501 2 6D0 491 . J 3 EDO B 1 502 1 EDO EDO . K 2 SAO C 1 501 3 SAO SAH . L 3 EDO C 1 502 4 EDO EDO . M 5 DXE C 1 503 7 DXE DXE . N 6 M2M C 1 504 9 M2M M2M . O 4 6D0 D 1 501 4 6D0 491 . P 3 EDO D 1 502 5 EDO EDO . Q 5 DXE D 1 503 8 DXE DXE . R 7 HOH A 1 601 119 HOH HOH . R 7 HOH A 2 602 37 HOH HOH . R 7 HOH A 3 603 60 HOH HOH . R 7 HOH A 4 604 30 HOH HOH . R 7 HOH A 5 605 48 HOH HOH . R 7 HOH A 6 606 92 HOH HOH . R 7 HOH A 7 607 32 HOH HOH . R 7 HOH A 8 608 73 HOH HOH . R 7 HOH A 9 609 26 HOH HOH . R 7 HOH A 10 610 50 HOH HOH . R 7 HOH A 11 611 28 HOH HOH . R 7 HOH A 12 612 99 HOH HOH . R 7 HOH A 13 613 118 HOH HOH . R 7 HOH A 14 614 96 HOH HOH . R 7 HOH A 15 615 88 HOH HOH . R 7 HOH A 16 616 120 HOH HOH . R 7 HOH A 17 617 103 HOH HOH . R 7 HOH A 18 618 15 HOH HOH . R 7 HOH A 19 619 54 HOH HOH . R 7 HOH A 20 620 57 HOH HOH . R 7 HOH A 21 621 97 HOH HOH . R 7 HOH A 22 622 27 HOH HOH . R 7 HOH A 23 623 53 HOH HOH . R 7 HOH A 24 624 20 HOH HOH . R 7 HOH A 25 625 72 HOH HOH . R 7 HOH A 26 626 83 HOH HOH . R 7 HOH A 27 627 34 HOH HOH . R 7 HOH A 28 628 25 HOH HOH . R 7 HOH A 29 629 71 HOH HOH . R 7 HOH A 30 630 62 HOH HOH . R 7 HOH A 31 631 106 HOH HOH . R 7 HOH A 32 632 80 HOH HOH . R 7 HOH A 33 633 100 HOH HOH . R 7 HOH A 34 634 93 HOH HOH . S 7 HOH B 1 601 87 HOH HOH . S 7 HOH B 2 602 3 HOH HOH . S 7 HOH B 3 603 78 HOH HOH . S 7 HOH B 4 604 75 HOH HOH . S 7 HOH B 5 605 70 HOH HOH . S 7 HOH B 6 606 21 HOH HOH . S 7 HOH B 7 607 16 HOH HOH . S 7 HOH B 8 608 17 HOH HOH . S 7 HOH B 9 609 102 HOH HOH . S 7 HOH B 10 610 91 HOH HOH . S 7 HOH B 11 611 23 HOH HOH . S 7 HOH B 12 612 51 HOH HOH . S 7 HOH B 13 613 82 HOH HOH . S 7 HOH B 14 614 98 HOH HOH . S 7 HOH B 15 615 22 HOH HOH . S 7 HOH B 16 616 69 HOH HOH . S 7 HOH B 17 617 116 HOH HOH . S 7 HOH B 18 618 38 HOH HOH . S 7 HOH B 19 619 101 HOH HOH . S 7 HOH B 20 620 109 HOH HOH . S 7 HOH B 21 621 86 HOH HOH . T 7 HOH C 1 601 29 HOH HOH . T 7 HOH C 2 602 67 HOH HOH . T 7 HOH C 3 603 43 HOH HOH . T 7 HOH C 4 604 74 HOH HOH . T 7 HOH C 5 605 117 HOH HOH . T 7 HOH C 6 606 11 HOH HOH . T 7 HOH C 7 607 1 HOH HOH . T 7 HOH C 8 608 2 HOH HOH . T 7 HOH C 9 609 6 HOH HOH . T 7 HOH C 10 610 5 HOH HOH . T 7 HOH C 11 611 104 HOH HOH . T 7 HOH C 12 612 79 HOH HOH . T 7 HOH C 13 613 84 HOH HOH . T 7 HOH C 14 614 85 HOH HOH . T 7 HOH C 15 615 95 HOH HOH . T 7 HOH C 16 616 4 HOH HOH . T 7 HOH C 17 617 113 HOH HOH . T 7 HOH C 18 618 59 HOH HOH . T 7 HOH C 19 619 24 HOH HOH . T 7 HOH C 20 620 90 HOH HOH . T 7 HOH C 21 621 12 HOH HOH . T 7 HOH C 22 622 64 HOH HOH . T 7 HOH C 23 623 18 HOH HOH . T 7 HOH C 24 624 47 HOH HOH . T 7 HOH C 25 625 10 HOH HOH . T 7 HOH C 26 626 14 HOH HOH . T 7 HOH C 27 627 52 HOH HOH . T 7 HOH C 28 628 76 HOH HOH . T 7 HOH C 29 629 89 HOH HOH . T 7 HOH C 30 630 41 HOH HOH . T 7 HOH C 31 631 45 HOH HOH . T 7 HOH C 32 632 31 HOH HOH . T 7 HOH C 33 633 111 HOH HOH . T 7 HOH C 34 634 56 HOH HOH . T 7 HOH C 35 635 108 HOH HOH . T 7 HOH C 36 636 55 HOH HOH . T 7 HOH C 37 637 63 HOH HOH . T 7 HOH C 38 638 44 HOH HOH . T 7 HOH C 39 639 40 HOH HOH . U 7 HOH D 1 601 107 HOH HOH . U 7 HOH D 2 602 81 HOH HOH . U 7 HOH D 3 603 66 HOH HOH . U 7 HOH D 4 604 61 HOH HOH . U 7 HOH D 5 605 33 HOH HOH . U 7 HOH D 6 606 77 HOH HOH . U 7 HOH D 7 607 7 HOH HOH . U 7 HOH D 8 608 94 HOH HOH . U 7 HOH D 9 609 42 HOH HOH . U 7 HOH D 10 610 8 HOH HOH . U 7 HOH D 11 611 68 HOH HOH . U 7 HOH D 12 612 13 HOH HOH . U 7 HOH D 13 613 58 HOH HOH . U 7 HOH D 14 614 19 HOH HOH . U 7 HOH D 15 615 39 HOH HOH . U 7 HOH D 16 616 49 HOH HOH . U 7 HOH D 17 617 110 HOH HOH . U 7 HOH D 18 618 114 HOH HOH . U 7 HOH D 19 619 105 HOH HOH . U 7 HOH D 20 620 9 HOH HOH . U 7 HOH D 21 621 115 HOH HOH . U 7 HOH D 22 622 112 HOH HOH . U 7 HOH D 23 623 46 HOH HOH . U 7 HOH D 24 624 35 HOH HOH . U 7 HOH D 25 625 65 HOH HOH . U 7 HOH D 26 626 36 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 O O1 6D0 . . . I 4 23.217 14.202 120.005 1 84.4 ? O1 6D0 501 B 1 HETATM 2 C C1 6D0 . . . I 4 23.925 15.209 119.936 1 84.22 ? C1 6D0 501 B 1 HETATM 3 C C2 6D0 . . . I 4 23.257 16.53 119.573 1 83.52 ? C2 6D0 501 B 1 HETATM 4 N N1 6D0 . . . I 4 21.948 16.585 120.108 1 83.42 ? N1 6D0 501 B 1 HETATM 5 C C3 6D0 . . . I 4 24.12 17.697 120.065 1 83.06 ? C3 6D0 501 B 1 HETATM 6 C C4 6D0 . . . I 4 23.926 18.196 121.48 1 82.97 ? C4 6D0 501 B 1 HETATM 7 N N2 6D0 . . . I 4 23.348 19.591 121.608 1 83.48 ? N2 6D0 501 B 1 HETATM 8 C C5 6D0 . . . I 4 24.334 20.732 121.26 1 78.7 ? C5 6D0 501 B 1 HETATM 9 C C6 6D0 . . . I 4 24.487 20.989 119.852 1 73.77 ? C6 6D0 501 B 1 HETATM 10 O O2 6D0 . . . I 4 23.535 21.961 119.364 1 70.79 ? O2 6D0 501 B 1 HETATM 11 C C7 6D0 . . . I 4 24.297 22.99 118.682 1 69.01 ? C7 6D0 501 B 1 HETATM 12 C C8 6D0 . . . I 4 25.671 22.956 119.297 1 69.96 ? C8 6D0 501 B 1 HETATM 13 O O3 6D0 . . . I 4 26.652 23.438 118.432 1 68.97 ? O3 6D0 501 B 1 HETATM 14 C C9 6D0 . . . I 4 25.888 21.538 119.566 1 72.03 ? C9 6D0 501 B 1 HETATM 15 O O4 6D0 . . . I 4 26.424 20.864 118.438 1 72.46 ? O4 6D0 501 B 1 HETATM 16 N N3 6D0 . . . I 4 23.643 24.244 118.839 1 66.08 ? N3 6D0 501 B 1 HETATM 17 C C10 6D0 . . . I 4 23.575 24.98 119.962 1 64.54 ? C10 6D0 501 B 1 HETATM 18 N N4 6D0 . . . I 4 22.879 26.081 119.744 1 63.41 ? N4 6D0 501 B 1 HETATM 19 C C11 6D0 . . . I 4 22.469 26.079 118.445 1 63.21 ? C11 6D0 501 B 1 HETATM 20 C C12 6D0 . . . I 4 21.706 26.947 117.598 1 62.23 ? C12 6D0 501 B 1 HETATM 21 N N5 6D0 . . . I 4 21.174 28.154 118.086 1 60.74 ? N5 6D0 501 B 1 HETATM 22 C C13 6D0 . . . I 4 22.957 24.894 117.868 1 64.34 ? C13 6D0 501 B 1 HETATM 23 N N6 6D0 . . . I 4 22.685 24.625 116.542 1 63.47 ? N6 6D0 501 B 1 HETATM 24 C C14 6D0 . . . I 4 21.968 25.48 115.803 1 62.62 ? C14 6D0 501 B 1 HETATM 25 N N7 6D0 . . . I 4 21.489 26.596 116.291 1 62.49 ? N7 6D0 501 B 1 HETATM 26 C C15 6D0 . . . I 4 22.865 19.774 122.952 1 88.99 ? C15 6D0 501 B 1 HETATM 27 C C16 6D0 . . . I 4 23.907 19.814 124.063 1 94.35 ? C16 6D0 501 B 1 HETATM 28 C C17 6D0 . . . I 4 23.474 19.759 125.544 1 98.6 ? C17 6D0 501 B 1 HETATM 29 O O5 6D0 . . . I 4 25.125 19.881 123.799 1 95.18 ? O5 6D0 501 B 1 HETATM 30 BR BR1 6D0 . . . I 4 24.892 19.085 126.704 1 103.47 ? BR1 6D0 501 B 1 HETATM 31 O O6 6D0 . . . I 4 25.237 15.196 120.165 1 84.64 ? O6 6D0 501 B 1 HETATM 32 H H1 6D0 . . . I 4 23.195 16.58 118.649 1 100.22 ? H1 6D0 501 B 1 HETATM 33 H H2 6D0 . . . I 4 21.47 15.829 119.846 1 100.11 ? H2 6D0 501 B 1 HETATM 34 H H3 6D0 . . . I 4 21.51 17.356 119.798 1 100.11 ? H3 6D0 501 B 1 HETATM 35 H H5 6D0 . . . I 4 23.973 18.468 119.45 1 99.68 ? H5 6D0 501 B 1 HETATM 36 H H6 6D0 . . . I 4 25.163 17.391 119.967 1 99.68 ? H6 6D0 501 B 1 HETATM 37 H H7 6D0 . . . I 4 23.374 17.591 121.943 1 99.56 ? H7 6D0 501 B 1 HETATM 38 H H8 6D0 . . . I 4 24.817 18.201 121.918 1 99.56 ? H8 6D0 501 B 1 HETATM 39 H H10 6D0 . . . I 4 25.204 20.494 121.612 1 94.44 ? H10 6D0 501 B 1 HETATM 40 H H11 6D0 . . . I 4 24.027 21.58 121.714 1 94.44 ? H11 6D0 501 B 1 HETATM 41 H H12 6D0 . . . I 4 24.373 20.171 119.373 1 88.53 ? H12 6D0 501 B 1 HETATM 42 H H13 6D0 . . . I 4 24.366 22.761 117.681 1 82.81 ? H13 6D0 501 B 1 HETATM 43 H H14 6D0 . . . I 4 25.679 23.426 120.071 1 83.95 ? H14 6D0 501 B 1 HETATM 44 H H15 6D0 . . . I 4 26.605 23.019 117.692 1 82.77 ? H15 6D0 501 B 1 HETATM 45 H H16 6D0 . . . I 4 26.484 21.415 120.365 1 86.44 ? H16 6D0 501 B 1 HETATM 46 H H17 6D0 . . . I 4 25.872 21.009 117.696 1 86.96 ? H17 6D0 501 B 1 HETATM 47 H H18 6D0 . . . I 4 23.987 24.738 120.82 1 77.45 ? H18 6D0 501 B 1 HETATM 48 H H19 6D0 . . . I 4 21.67 28.677 118.722 1 72.89 ? H19 6D0 501 B 1 HETATM 49 H H20 6D0 . . . I 4 20.397 28.426 117.812 1 72.89 ? H20 6D0 501 B 1 HETATM 50 H H21 6D0 . . . I 4 21.782 25.251 114.813 1 75.14 ? H21 6D0 501 B 1 HETATM 51 H H22 6D0 . . . I 4 22.277 19.06 123.141 1 106.79 ? H22 6D0 501 B 1 HETATM 52 H H23 6D0 . . . I 4 22.373 20.575 122.979 1 106.79 ? H23 6D0 501 B 1 HETATM 53 H H24 6D0 . . . I 4 23.227 20.67 125.84 1 118.33 ? H24 6D0 501 B 1 HETATM 54 H H25 6D0 . . . I 4 22.616 19.117 125.633 1 118.33 ? H25 6D0 501 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 54 #