data_6DW7 # _model_server_result.job_id J3zHiy_zubNqalDVehaZhA _model_server_result.datetime_utc '2024-11-24 16:09:02' _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 6dw7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 6DW7 # _exptl.entry_id 6DW7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.67 _cell.angle_gamma 90 _cell.entry_id 6DW7 _cell.length_a 84.546 _cell.length_b 146.372 _cell.length_c 98.929 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DW7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 ? 2 E N N ? 2 M N N ? 2 N N N ? 2 U N 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 metalc ? metalc1 A O THR 38 A THR 114 1_555 J NA NA . A NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc2 A OD2 ASP 235 A ASP 311 1_555 I NA NA . A NA 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc3 E O1G DTP . A DTP 701 1_555 K MG MG . B MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc4 E O1B DTP . A DTP 701 1_555 K MG MG . B MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc5 F MG MG . A MG 702 1_555 G O1A GTP . A GTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc6 F MG MG . A MG 702 1_555 G O1B GTP . A GTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc7 F MG MG . A MG 702 1_555 G O1G GTP . A GTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc8 F MG MG . A MG 702 1_555 M O1B DTP . B DTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc9 F MG MG . A MG 702 1_555 M O3G DTP . B DTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc10 I NA NA . A NA 705 1_555 W O HOH . A HOH 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc11 J NA NA . A NA 706 1_555 W O HOH . A HOH 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc12 K MG MG . B MG 701 1_555 L O2B GTP . B GTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc13 K MG MG . B MG 701 1_555 L O2A GTP . B GTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc14 K MG MG . B MG 701 1_555 L O2G GTP . B GTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.65 sing metalc ? metalc15 C O GLN 434 C GLN 510 1_555 S NA NA . C NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc16 C O LYS 436 C LYS 512 1_555 S NA NA . C NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc17 N O3G DTP . C DTP 701 1_555 O MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc18 N O2B DTP . C DTP 701 1_555 O MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc19 O MG MG . C MG 702 1_555 T O1G GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc20 O MG MG . C MG 702 1_555 T O1B GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc21 O MG MG . C MG 702 1_555 T O3A GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc22 P MG MG . C MG 703 1_555 Q O2A GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc23 P MG MG . C MG 703 1_555 Q O2B GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc24 P MG MG . C MG 703 1_555 Q O2G GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.689 sing metalc ? metalc25 P MG MG . C MG 703 1_555 U O1G DTP . D DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc26 P MG MG . C MG 703 1_555 U O2B DTP . D DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _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 PG O1G DTP doub 83 n n PG O2G DTP sing 84 n n PG O3G DTP sing 85 n n PG O3B DTP sing 86 n n O2G HOG2 DTP sing 87 n n O3G HOG3 DTP sing 88 n n PB O1B DTP doub 89 n n PB O2B DTP sing 90 n n PB O3B DTP sing 91 n n PB O3A DTP sing 92 n n O2B HOB2 DTP sing 93 n n PA O1A DTP doub 94 n n PA O2A DTP sing 95 n n PA O3A DTP sing 96 n n PA O5' DTP sing 97 n n O2A HOA2 DTP sing 98 n n O5' C5' DTP sing 99 n n C5' C4' DTP sing 100 n n C5' "H5'1" DTP sing 101 n n C5' "H5'2" DTP sing 102 n n C4' O4' DTP sing 103 n n C4' C3' DTP sing 104 n n C4' H4' DTP sing 105 n n O4' C1' DTP sing 106 n n C3' O3' DTP sing 107 n n C3' C2' DTP sing 108 n n C3' H3' DTP sing 109 n n O3' HO3' DTP sing 110 n n C2' C1' DTP sing 111 n n C2' "H2'1" DTP sing 112 n n C2' "H2'2" DTP sing 113 n n C1' N9 DTP sing 114 n n C1' H1' DTP sing 115 n n N9 C8 DTP sing 116 n y N9 C4 DTP sing 117 n y C8 N7 DTP doub 118 n y C8 H8 DTP sing 119 n n N7 C5 DTP sing 120 n y C5 C6 DTP sing 121 n y C5 C4 DTP doub 122 n y C6 N6 DTP sing 123 n n C6 N1 DTP doub 124 n y N6 HN61 DTP sing 125 n n N6 HN62 DTP sing 126 n n N1 C2 DTP sing 127 n y C2 N3 DTP doub 128 n y C2 H2 DTP sing 129 n n N3 C4 DTP sing 130 n y # _atom_sites.entry_id 6DW7 _atom_sites.fract_transf_matrix[1][1] 0.011828 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005186 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006832 _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] 0.011037 _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 DTP A 1 701 800 DTP DTP . F 3 MG A 1 702 850 MG MG . G 4 GTP A 1 703 900 GTP GTP . H 5 GLY A 1 704 2 GLY GLY . I 6 NA A 1 705 2 NA NA . J 6 NA A 1 706 3 NA NA . K 3 MG B 1 701 850 MG MG . L 4 GTP B 1 702 900 GTP GTP . M 2 DTP B 1 703 800 DTP DTP . N 2 DTP C 1 701 800 DTP DTP . O 3 MG C 1 702 850 MG MG . P 3 MG C 1 703 850 MG MG . Q 4 GTP C 1 704 900 GTP GTP . R 5 GLY C 1 705 1 GLY GLY . S 6 NA C 1 706 1 NA NA . T 4 GTP D 1 701 900 GTP GTP . U 2 DTP D 1 702 800 DTP DTP . V 7 PO4 D 1 703 1 PO4 PO4 . W 8 HOH A 1 801 29 HOH HOH . W 8 HOH A 2 802 35 HOH HOH . W 8 HOH A 3 803 22 HOH HOH . W 8 HOH A 4 804 21 HOH HOH . W 8 HOH A 5 805 19 HOH HOH . W 8 HOH A 6 806 53 HOH HOH . W 8 HOH A 7 807 20 HOH HOH . W 8 HOH A 8 808 31 HOH HOH . W 8 HOH A 9 809 56 HOH HOH . W 8 HOH A 10 810 7 HOH HOH . W 8 HOH A 11 811 54 HOH HOH . W 8 HOH A 12 812 55 HOH HOH . W 8 HOH A 13 813 3 HOH HOH . W 8 HOH A 14 814 52 HOH HOH . X 8 HOH B 1 801 14 HOH HOH . X 8 HOH B 2 802 9 HOH HOH . X 8 HOH B 3 803 38 HOH HOH . X 8 HOH B 4 804 2 HOH HOH . X 8 HOH B 5 805 8 HOH HOH . X 8 HOH B 6 806 15 HOH HOH . X 8 HOH B 7 807 30 HOH HOH . X 8 HOH B 8 808 28 HOH HOH . X 8 HOH B 9 809 37 HOH HOH . X 8 HOH B 10 810 25 HOH HOH . X 8 HOH B 11 811 42 HOH HOH . X 8 HOH B 12 812 12 HOH HOH . X 8 HOH B 13 813 57 HOH HOH . X 8 HOH B 14 814 1 HOH HOH . X 8 HOH B 15 815 48 HOH HOH . X 8 HOH B 16 816 44 HOH HOH . X 8 HOH B 17 817 46 HOH HOH . X 8 HOH B 18 818 16 HOH HOH . Y 8 HOH C 1 801 4 HOH HOH . Y 8 HOH C 2 802 43 HOH HOH . Y 8 HOH C 3 803 18 HOH HOH . Y 8 HOH C 4 804 34 HOH HOH . Y 8 HOH C 5 805 32 HOH HOH . Y 8 HOH C 6 806 11 HOH HOH . Y 8 HOH C 7 807 13 HOH HOH . Y 8 HOH C 8 808 50 HOH HOH . Y 8 HOH C 9 809 17 HOH HOH . Y 8 HOH C 10 810 26 HOH HOH . Y 8 HOH C 11 811 24 HOH HOH . Y 8 HOH C 12 812 45 HOH HOH . Y 8 HOH C 13 813 49 HOH HOH . Z 8 HOH D 1 801 39 HOH HOH . Z 8 HOH D 2 802 40 HOH HOH . Z 8 HOH D 3 803 36 HOH HOH . Z 8 HOH D 4 804 51 HOH HOH . Z 8 HOH D 5 805 33 HOH HOH . Z 8 HOH D 6 806 27 HOH HOH . Z 8 HOH D 7 807 58 HOH HOH . Z 8 HOH D 8 808 60 HOH HOH . Z 8 HOH D 9 809 47 HOH HOH . Z 8 HOH D 10 810 41 HOH HOH . Z 8 HOH D 11 811 59 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 P PG DTP . . . E 2 1.773 7.541 -35.852 1 42.81 ? PG DTP 701 A 1 HETATM 2 O O1G DTP . . . E 2 2.313 7.815 -37.252 1 34.71 ? O1G DTP 701 A 1 HETATM 3 O O2G DTP . . . E 2 0.315 7.093 -35.811 1 44.15 ? O2G DTP 701 A 1 HETATM 4 O O3G DTP . . . E 2 2.157 8.63 -34.908 1 41.28 ? O3G DTP 701 A 1 HETATM 5 P PB DTP . . . E 2 3.723 5.375 -35.596 1 35.25 ? PB DTP 701 A 1 HETATM 6 O O1B DTP . . . E 2 4.692 6.23 -36.384 1 38.56 ? O1B DTP 701 A 1 HETATM 7 O O2B DTP . . . E 2 3.15 4.131 -36.161 1 34.12 ? O2B DTP 701 A 1 HETATM 8 O O3B DTP . . . E 2 2.493 6.302 -35.075 1 37.45 ? O3B DTP 701 A 1 HETATM 9 P PA DTP . . . E 2 4.18 4.418 -32.847 1 36.12 ? PA DTP 701 A 1 HETATM 10 O O1A DTP . . . E 2 3.246 3.228 -32.932 1 36.28 ? O1A DTP 701 A 1 HETATM 11 O O2A DTP . . . E 2 3.986 5.602 -31.916 1 34.59 ? O2A DTP 701 A 1 HETATM 12 O O3A DTP . . . E 2 4.575 5.065 -34.26 1 36.69 ? O3A DTP 701 A 1 HETATM 13 O O5' DTP . . . E 2 5.577 3.719 -32.482 1 36.16 ? O5' DTP 701 A 1 HETATM 14 C C5' DTP . . . E 2 6.8 4.459 -32.366 1 34.78 ? C5' DTP 701 A 1 HETATM 15 C C4' DTP . . . E 2 7.906 3.587 -31.768 1 36.64 ? C4' DTP 701 A 1 HETATM 16 O O4' DTP . . . E 2 7.441 3.02 -30.548 1 36.81 ? O4' DTP 701 A 1 HETATM 17 C C3' DTP . . . E 2 8.313 2.4 -32.611 1 38.21 ? C3' DTP 701 A 1 HETATM 18 O O3' DTP . . . E 2 9.693 2.113 -32.325 1 44.57 ? O3' DTP 701 A 1 HETATM 19 C C2' DTP . . . E 2 7.485 1.228 -32.143 1 35.97 ? C2' DTP 701 A 1 HETATM 20 C C1' DTP . . . E 2 7.232 1.636 -30.693 1 40.81 ? C1' DTP 701 A 1 HETATM 21 N N9 DTP . . . E 2 5.904 1.418 -30.103 1 41.42 ? N9 DTP 701 A 1 HETATM 22 C C8 DTP . . . E 2 4.69 1.43 -30.658 1 44.13 ? C8 DTP 701 A 1 HETATM 23 N N7 DTP . . . E 2 3.722 1.154 -29.739 1 46.92 ? N7 DTP 701 A 1 HETATM 24 C C5 DTP . . . E 2 4.343 0.991 -28.558 1 45.2 ? C5 DTP 701 A 1 HETATM 25 C C6 DTP . . . E 2 3.955 0.734 -27.162 1 40.64 ? C6 DTP 701 A 1 HETATM 26 N N6 DTP . . . E 2 2.688 0.584 -26.738 1 37.7 ? N6 DTP 701 A 1 HETATM 27 N N1 DTP . . . E 2 4.948 0.655 -26.291 1 42.08 ? N1 DTP 701 A 1 HETATM 28 C C2 DTP . . . E 2 6.255 0.81 -26.583 1 43.63 ? C2 DTP 701 A 1 HETATM 29 N N3 DTP . . . E 2 6.686 1.073 -27.81 1 45.07 ? N3 DTP 701 A 1 HETATM 30 C C4 DTP . . . E 2 5.785 1.169 -28.815 1 45.34 ? C4 DTP 701 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 30 #