data_4TYW # _model_server_result.job_id yMYTRJhm5_jmgnReszRyPA _model_server_result.datetime_utc '2024-11-05 01:23:05' _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 4tyw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":604}' # _entry.id 4TYW # _exptl.entry_id 4TYW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 4TYW _cell.length_a 89.829 _cell.length_b 126.26 _cell.length_c 55.545 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TYW _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 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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 PHE 356 A PHE 442 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc2 A O ARG 380 A ARG 466 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc3 C MG MG . A MG 601 1_555 F O2B ADP . A ADP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 C MG MG . A MG 601 1_555 G O HOH . A HOH 799 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc5 C MG MG . A MG 601 1_555 G O HOH . A HOH 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc6 C MG MG . A MG 601 1_555 G O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc7 C MG MG . A MG 601 1_555 G O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc8 D MG MG . A MG 602 1_555 G O HOH . A HOH 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 40 n n PB O2B ADP sing 41 n n PB O3B ADP sing 42 n n PB O3A ADP sing 43 n n O2B HOB2 ADP sing 44 n n O3B HOB3 ADP sing 45 n n PA O1A ADP doub 46 n n PA O2A ADP sing 47 n n PA O3A ADP sing 48 n n PA O5' ADP sing 49 n n O2A HOA2 ADP sing 50 n n O5' C5' ADP sing 51 n n C5' C4' ADP sing 52 n n C5' "H5'1" ADP sing 53 n n C5' "H5'2" ADP sing 54 n n C4' O4' ADP sing 55 n n C4' C3' ADP sing 56 n n C4' H4' ADP sing 57 n n O4' C1' ADP sing 58 n n C3' O3' ADP sing 59 n n C3' C2' ADP sing 60 n n C3' H3' ADP sing 61 n n O3' HO3' ADP sing 62 n n C2' O2' ADP sing 63 n n C2' C1' ADP sing 64 n n C2' H2' ADP sing 65 n n O2' HO2' ADP sing 66 n n C1' N9 ADP sing 67 n n C1' H1' ADP sing 68 n n N9 C8 ADP sing 69 n y N9 C4 ADP sing 70 n y C8 N7 ADP doub 71 n y C8 H8 ADP sing 72 n n N7 C5 ADP sing 73 n y C5 C6 ADP sing 74 n y C5 C4 ADP doub 75 n y C6 N6 ADP sing 76 n n C6 N1 ADP doub 77 n y N6 HN61 ADP sing 78 n n N6 HN62 ADP sing 79 n n N1 C2 ADP sing 80 n y C2 N3 ADP doub 81 n y C2 H2 ADP sing 82 n n N3 C4 ADP sing 83 n y # _atom_sites.entry_id 4TYW _atom_sites.fract_transf_matrix[1][1] 0.011132 _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] 0.00792 _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] 0.018003 _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 3 MG A 1 601 1 MG MG . D 3 MG A 1 602 3 MG MG . E 4 BEF A 1 603 900 BEF BEF . F 5 ADP A 1 604 1000 ADP ADP . G 6 HOH A 1 701 61 HOH HOH . G 6 HOH A 2 702 75 HOH HOH . G 6 HOH A 3 703 99 HOH HOH . G 6 HOH A 4 704 96 HOH HOH . G 6 HOH A 5 705 73 HOH HOH . G 6 HOH A 6 706 89 HOH HOH . G 6 HOH A 7 707 108 HOH HOH . G 6 HOH A 8 708 14 HOH HOH . G 6 HOH A 9 709 28 HOH HOH . G 6 HOH A 10 710 1 HOH HOH . G 6 HOH A 11 711 3 HOH HOH . G 6 HOH A 12 712 4 HOH HOH . G 6 HOH A 13 713 5 HOH HOH . G 6 HOH A 14 714 6 HOH HOH . G 6 HOH A 15 715 7 HOH HOH . G 6 HOH A 16 716 8 HOH HOH . G 6 HOH A 17 717 9 HOH HOH . G 6 HOH A 18 718 10 HOH HOH . G 6 HOH A 19 719 11 HOH HOH . G 6 HOH A 20 720 13 HOH HOH . G 6 HOH A 21 721 15 HOH HOH . G 6 HOH A 22 722 16 HOH HOH . G 6 HOH A 23 723 17 HOH HOH . G 6 HOH A 24 724 18 HOH HOH . G 6 HOH A 25 725 19 HOH HOH . G 6 HOH A 26 726 20 HOH HOH . G 6 HOH A 27 727 21 HOH HOH . G 6 HOH A 28 728 22 HOH HOH . G 6 HOH A 29 729 23 HOH HOH . G 6 HOH A 30 730 24 HOH HOH . G 6 HOH A 31 731 25 HOH HOH . G 6 HOH A 32 732 26 HOH HOH . G 6 HOH A 33 733 27 HOH HOH . G 6 HOH A 34 734 29 HOH HOH . G 6 HOH A 35 735 30 HOH HOH . G 6 HOH A 36 736 31 HOH HOH . G 6 HOH A 37 737 32 HOH HOH . G 6 HOH A 38 738 33 HOH HOH . G 6 HOH A 39 739 34 HOH HOH . G 6 HOH A 40 740 35 HOH HOH . G 6 HOH A 41 741 37 HOH HOH . G 6 HOH A 42 742 38 HOH HOH . G 6 HOH A 43 743 39 HOH HOH . G 6 HOH A 44 744 44 HOH HOH . G 6 HOH A 45 745 45 HOH HOH . G 6 HOH A 46 746 47 HOH HOH . G 6 HOH A 47 747 51 HOH HOH . G 6 HOH A 48 748 53 HOH HOH . G 6 HOH A 49 749 55 HOH HOH . G 6 HOH A 50 750 57 HOH HOH . G 6 HOH A 51 751 58 HOH HOH . G 6 HOH A 52 752 59 HOH HOH . G 6 HOH A 53 753 60 HOH HOH . G 6 HOH A 54 754 62 HOH HOH . G 6 HOH A 55 755 63 HOH HOH . G 6 HOH A 56 756 64 HOH HOH . G 6 HOH A 57 757 65 HOH HOH . G 6 HOH A 58 758 66 HOH HOH . G 6 HOH A 59 759 67 HOH HOH . G 6 HOH A 60 760 68 HOH HOH . G 6 HOH A 61 761 69 HOH HOH . G 6 HOH A 62 762 70 HOH HOH . G 6 HOH A 63 763 71 HOH HOH . G 6 HOH A 64 764 72 HOH HOH . G 6 HOH A 65 765 76 HOH HOH . G 6 HOH A 66 766 77 HOH HOH . G 6 HOH A 67 767 78 HOH HOH . G 6 HOH A 68 768 80 HOH HOH . G 6 HOH A 69 769 81 HOH HOH . G 6 HOH A 70 770 83 HOH HOH . G 6 HOH A 71 771 84 HOH HOH . G 6 HOH A 72 772 85 HOH HOH . G 6 HOH A 73 773 86 HOH HOH . G 6 HOH A 74 774 88 HOH HOH . G 6 HOH A 75 775 92 HOH HOH . G 6 HOH A 76 776 93 HOH HOH . G 6 HOH A 77 777 94 HOH HOH . G 6 HOH A 78 778 95 HOH HOH . G 6 HOH A 79 779 97 HOH HOH . G 6 HOH A 80 780 98 HOH HOH . G 6 HOH A 81 781 101 HOH HOH . G 6 HOH A 82 782 102 HOH HOH . G 6 HOH A 83 783 103 HOH HOH . G 6 HOH A 84 784 105 HOH HOH . G 6 HOH A 85 785 106 HOH HOH . G 6 HOH A 86 786 109 HOH HOH . G 6 HOH A 87 787 111 HOH HOH . G 6 HOH A 88 788 113 HOH HOH . G 6 HOH A 89 789 114 HOH HOH . G 6 HOH A 90 790 120 HOH HOH . G 6 HOH A 91 791 121 HOH HOH . G 6 HOH A 92 792 122 HOH HOH . G 6 HOH A 93 793 123 HOH HOH . G 6 HOH A 94 794 124 HOH HOH . G 6 HOH A 95 795 126 HOH HOH . G 6 HOH A 96 796 127 HOH HOH . G 6 HOH A 97 797 128 HOH HOH . G 6 HOH A 98 798 130 HOH HOH . G 6 HOH A 99 799 131 HOH HOH . G 6 HOH A 100 800 132 HOH HOH . G 6 HOH A 101 801 133 HOH HOH . G 6 HOH A 102 802 134 HOH HOH . G 6 HOH A 103 803 135 HOH HOH . G 6 HOH A 104 804 136 HOH HOH . G 6 HOH A 105 805 137 HOH HOH . G 6 HOH A 106 806 138 HOH HOH . G 6 HOH A 107 807 139 HOH HOH . G 6 HOH A 108 808 140 HOH HOH . G 6 HOH A 109 809 141 HOH HOH . G 6 HOH A 110 810 142 HOH HOH . G 6 HOH A 111 811 143 HOH HOH . G 6 HOH A 112 812 145 HOH HOH . G 6 HOH A 113 813 146 HOH HOH . H 6 HOH B 1 101 46 HOH HOH . H 6 HOH B 2 102 129 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 PB ADP . . . F 5 -26.553 30.667 -17.164 1 40.85 ? PB ADP 604 A 1 HETATM 2 O O1B ADP . . . F 5 -25.885 29.324 -16.995 1 45.29 ? O1B ADP 604 A 1 HETATM 3 O O2B ADP . . . F 5 -27.495 31.031 -16.043 1 35.17 ? O2B ADP 604 A 1 HETATM 4 O O3B ADP . . . F 5 -27.084 30.942 -18.548 1 38.76 ? O3B ADP 604 A 1 HETATM 5 P PA ADP . . . F 5 -24.854 32.193 -15.549 1 40.44 ? PA ADP 604 A 1 HETATM 6 O O1A ADP . . . F 5 -25.698 33.38 -15.147 1 37.3 ? O1A ADP 604 A 1 HETATM 7 O O2A ADP . . . F 5 -24.772 30.968 -14.673 1 38.47 ? O2A ADP 604 A 1 HETATM 8 O O3A ADP . . . F 5 -25.337 31.709 -17.006 1 42.78 ? O3A ADP 604 A 1 HETATM 9 O O5' ADP . . . F 5 -23.355 32.698 -15.853 1 42.96 ? O5' ADP 604 A 1 HETATM 10 C C5' ADP . . . F 5 -22.259 32.099 -15.167 1 43.58 ? C5' ADP 604 A 1 HETATM 11 C C4' ADP . . . F 5 -20.983 32.902 -15.385 1 42.67 ? C4' ADP 604 A 1 HETATM 12 O O4' ADP . . . F 5 -21.046 33.682 -16.582 1 41.13 ? O4' ADP 604 A 1 HETATM 13 C C3' ADP . . . F 5 -20.729 33.877 -14.246 1 42.64 ? C3' ADP 604 A 1 HETATM 14 O O3' ADP . . . F 5 -19.754 33.33 -13.354 1 44.43 ? O3' ADP 604 A 1 HETATM 15 C C2' ADP . . . F 5 -20.251 35.162 -14.9 1 47.09 ? C2' ADP 604 A 1 HETATM 16 O O2' ADP . . . F 5 -18.926 35.513 -14.484 1 63.42 ? O2' ADP 604 A 1 HETATM 17 C C1' ADP . . . F 5 -20.281 34.874 -16.395 1 49.87 ? C1' ADP 604 A 1 HETATM 18 N N9 ADP . . . F 5 -20.855 36.008 -17.161 1 50.06 ? N9 ADP 604 A 1 HETATM 19 C C8 ADP . . . F 5 -22.081 36.545 -17.012 1 48.96 ? C8 ADP 604 A 1 HETATM 20 N N7 ADP . . . F 5 -22.263 37.571 -17.883 1 48.16 ? N7 ADP 604 A 1 HETATM 21 C C5 ADP . . . F 5 -21.133 37.696 -18.604 1 53.43 ? C5 ADP 604 A 1 HETATM 22 C C6 ADP . . . F 5 -20.648 38.574 -19.692 1 52.13 ? C6 ADP 604 A 1 HETATM 23 N N6 ADP . . . F 5 -21.441 39.549 -20.187 1 54.41 ? N6 ADP 604 A 1 HETATM 24 N N1 ADP . . . F 5 -19.4 38.367 -20.164 1 55.9 ? N1 ADP 604 A 1 HETATM 25 C C2 ADP . . . F 5 -18.603 37.399 -19.676 1 57.51 ? C2 ADP 604 A 1 HETATM 26 N N3 ADP . . . F 5 -18.984 36.568 -18.689 1 50.39 ? N3 ADP 604 A 1 HETATM 27 C C4 ADP . . . F 5 -20.209 36.666 -18.123 1 49.1 ? C4 ADP 604 A 1 HETATM 28 H "H5'1" ADP . . . F 5 -22.116 31.079 -15.528 1 52.29 ? "H5'1" ADP 604 A 1 HETATM 29 H "H5'2" ADP . . . F 5 -22.481 32.049 -14.098 1 52.29 ? "H5'2" ADP 604 A 1 HETATM 30 H H4' ADP . . . F 5 -20.136 32.203 -15.443 1 51.2 ? H4' ADP 604 A 1 HETATM 31 H H3' ADP . . . F 5 -21.672 34.068 -13.715 1 51.17 ? H3' ADP 604 A 1 HETATM 32 H HO3' ADP . . . F 5 -19.594 33.951 -12.631 1 53.31 ? HO3' ADP 604 A 1 HETATM 33 H H2' ADP . . . F 5 -20.956 35.973 -14.67 1 56.51 ? H2' ADP 604 A 1 HETATM 34 H HO2' ADP . . . F 5 -18.917 35.66 -13.528 1 76.1 ? HO2' ADP 604 A 1 HETATM 35 H H1' ADP . . . F 5 -19.25 34.698 -16.73 1 59.84 ? H1' ADP 604 A 1 HETATM 36 H H8 ADP . . . F 5 -22.82 36.205 -16.297 1 58.75 ? H8 ADP 604 A 1 HETATM 37 H HN61 ADP . . . F 5 -21.105 40.145 -20.93 1 65.3 ? HN61 ADP 604 A 1 HETATM 38 H HN62 ADP . . . F 5 -22.371 39.681 -19.816 1 65.3 ? HN62 ADP 604 A 1 HETATM 39 H H2 ADP . . . F 5 -17.611 37.283 -20.096 1 69.02 ? H2 ADP 604 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 39 #