data_5ZDK # _model_server_result.job_id 21AWsEfnaloW2a28dp-JuQ _model_server_result.datetime_utc '2024-11-21 22:58:20' _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 5zdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5ZDK # _exptl.entry_id 5ZDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 116.48 _cell.angle_gamma 90 _cell.entry_id 5ZDK _cell.length_a 144.66 _cell.length_b 39.413 _cell.length_c 116.051 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 PRO 367 A PRO 367 1_555 C CS CS . A CS 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc2 A O ILE 370 A ILE 370 1_555 C CS CS . A CS 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? metalc ? metalc3 A O LYS 372 A LYS 372 1_555 C CS CS . A CS 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.213 ? metalc ? metalc4 B O1B ATP . A ATP 601 1_555 D CS CS . A CS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.005 ? metalc ? metalc5 B O2B ATP . A ATP 601 1_555 E MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc6 B O2A ATP . A ATP 601 1_555 E MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc7 B O1G ATP . A ATP 601 1_555 F MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-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 ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 5ZDK _atom_sites.fract_transf_matrix[1][1] 0.006913 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003444 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025372 _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] 0.009627 _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 B 2 ATP A 1 601 1 ATP ATP . C 3 CS A 1 602 1 CS CS . D 3 CS A 1 603 2 CS CS . E 4 MG A 1 604 1 MG MG . F 4 MG A 1 605 2 MG MG . G 5 CL A 1 606 1 CL CL . H 5 CL A 1 607 2 CL CL . I 6 HOH A 1 701 38 HOH HOH . I 6 HOH A 2 702 46 HOH HOH . I 6 HOH A 3 703 52 HOH HOH . I 6 HOH A 4 704 21 HOH HOH . I 6 HOH A 5 705 76 HOH HOH . I 6 HOH A 6 706 73 HOH HOH . I 6 HOH A 7 707 17 HOH HOH . I 6 HOH A 8 708 59 HOH HOH . I 6 HOH A 9 709 44 HOH HOH . I 6 HOH A 10 710 4 HOH HOH . I 6 HOH A 11 711 70 HOH HOH . I 6 HOH A 12 712 1 HOH HOH . I 6 HOH A 13 713 45 HOH HOH . I 6 HOH A 14 714 6 HOH HOH . I 6 HOH A 15 715 48 HOH HOH . I 6 HOH A 16 716 66 HOH HOH . I 6 HOH A 17 717 43 HOH HOH . I 6 HOH A 18 718 30 HOH HOH . I 6 HOH A 19 719 14 HOH HOH . I 6 HOH A 20 720 20 HOH HOH . I 6 HOH A 21 721 47 HOH HOH . I 6 HOH A 22 722 23 HOH HOH . I 6 HOH A 23 723 29 HOH HOH . I 6 HOH A 24 724 65 HOH HOH . I 6 HOH A 25 725 62 HOH HOH . I 6 HOH A 26 726 50 HOH HOH . I 6 HOH A 27 727 41 HOH HOH . I 6 HOH A 28 728 58 HOH HOH . I 6 HOH A 29 729 3 HOH HOH . I 6 HOH A 30 730 22 HOH HOH . I 6 HOH A 31 731 51 HOH HOH . I 6 HOH A 32 732 71 HOH HOH . I 6 HOH A 33 733 39 HOH HOH . I 6 HOH A 34 734 32 HOH HOH . I 6 HOH A 35 735 64 HOH HOH . I 6 HOH A 36 736 18 HOH HOH . I 6 HOH A 37 737 61 HOH HOH . I 6 HOH A 38 738 34 HOH HOH . I 6 HOH A 39 739 12 HOH HOH . I 6 HOH A 40 740 13 HOH HOH . I 6 HOH A 41 741 54 HOH HOH . I 6 HOH A 42 742 69 HOH HOH . I 6 HOH A 43 743 37 HOH HOH . I 6 HOH A 44 744 56 HOH HOH . I 6 HOH A 45 745 35 HOH HOH . I 6 HOH A 46 746 19 HOH HOH . I 6 HOH A 47 747 25 HOH HOH . I 6 HOH A 48 748 36 HOH HOH . I 6 HOH A 49 749 55 HOH HOH . I 6 HOH A 50 750 7 HOH HOH . I 6 HOH A 51 751 8 HOH HOH . I 6 HOH A 52 752 31 HOH HOH . I 6 HOH A 53 753 11 HOH HOH . I 6 HOH A 54 754 15 HOH HOH . I 6 HOH A 55 755 77 HOH HOH . I 6 HOH A 56 756 67 HOH HOH . I 6 HOH A 57 757 49 HOH HOH . I 6 HOH A 58 758 75 HOH HOH . I 6 HOH A 59 759 81 HOH HOH . I 6 HOH A 60 760 16 HOH HOH . I 6 HOH A 61 761 57 HOH HOH . I 6 HOH A 62 762 79 HOH HOH . I 6 HOH A 63 763 28 HOH HOH . I 6 HOH A 64 764 80 HOH HOH . I 6 HOH A 65 765 26 HOH HOH . I 6 HOH A 66 766 74 HOH HOH . I 6 HOH A 67 767 2 HOH HOH . I 6 HOH A 68 768 63 HOH HOH . I 6 HOH A 69 769 78 HOH HOH . I 6 HOH A 70 770 60 HOH HOH . I 6 HOH A 71 771 42 HOH HOH . I 6 HOH A 72 772 68 HOH HOH . I 6 HOH A 73 773 82 HOH HOH . I 6 HOH A 74 774 5 HOH HOH . I 6 HOH A 75 775 10 HOH HOH . I 6 HOH A 76 776 40 HOH HOH . I 6 HOH A 77 777 53 HOH HOH . I 6 HOH A 78 778 9 HOH HOH . I 6 HOH A 79 779 72 HOH HOH . I 6 HOH A 80 780 27 HOH HOH . I 6 HOH A 81 781 33 HOH HOH . I 6 HOH A 82 782 24 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 ATP . . . B 2 20.608 6.082 17.536 0.88 41.72 ? PG ATP 601 A 1 HETATM 2 O O1G ATP . . . B 2 21.344 6.702 16.346 0.88 44.98 ? O1G ATP 601 A 1 HETATM 3 O O2G ATP . . . B 2 21.324 6.16 18.853 0.88 47.05 ? O2G ATP 601 A 1 HETATM 4 O O3G ATP . . . B 2 19.138 6.363 17.681 0.88 43.13 ? O3G ATP 601 A 1 HETATM 5 P PB ATP . . . B 2 22.114 3.943 16.554 0.88 43.15 ? PB ATP 601 A 1 HETATM 6 O O1B ATP . . . B 2 22.065 3.886 15.018 0.88 43.95 ? O1B ATP 601 A 1 HETATM 7 O O2B ATP . . . B 2 23.2 4.668 17.359 0.88 40.69 ? O2B ATP 601 A 1 HETATM 8 O O3B ATP . . . B 2 20.713 4.536 17.09 0.88 48.39 ? O3B ATP 601 A 1 HETATM 9 P PA ATP . . . B 2 22.608 1.795 18.346 0.88 42.78 ? PA ATP 601 A 1 HETATM 10 O O1A ATP . . . B 2 23.417 0.762 17.632 0.88 42.24 ? O1A ATP 601 A 1 HETATM 11 O O2A ATP . . . B 2 23.225 2.955 19.113 0.88 47.94 ? O2A ATP 601 A 1 HETATM 12 O O3A ATP . . . B 2 21.904 2.421 17.061 0.88 48.1 ? O3A ATP 601 A 1 HETATM 13 O O5' ATP . . . B 2 21.272 1.297 19.118 0.88 47.36 ? O5' ATP 601 A 1 HETATM 14 C C5' ATP . . . B 2 20.396 0.284 18.596 0.88 43.57 ? C5' ATP 601 A 1 HETATM 15 C C4' ATP . . . B 2 18.928 0.524 18.953 0.88 40.05 ? C4' ATP 601 A 1 HETATM 16 O O4' ATP . . . B 2 18.79 0.931 20.32 0.88 43.34 ? O4' ATP 601 A 1 HETATM 17 C C3' ATP . . . B 2 18.368 1.659 18.15 0.88 42.27 ? C3' ATP 601 A 1 HETATM 18 O O3' ATP . . . B 2 16.989 1.353 17.939 0.88 39.34 ? O3' ATP 601 A 1 HETATM 19 C C2' ATP . . . B 2 18.58 2.875 19.058 0.88 42.15 ? C2' ATP 601 A 1 HETATM 20 O O2' ATP . . . B 2 17.806 4.065 18.754 0.88 44.57 ? O2' ATP 601 A 1 HETATM 21 C C1' ATP . . . B 2 18.242 2.255 20.4 0.88 38.79 ? C1' ATP 601 A 1 HETATM 22 N N9 ATP . . . B 2 18.76 3.169 21.447 0.88 35.49 ? N9 ATP 601 A 1 HETATM 23 C C8 ATP . . . B 2 19.948 3.82 21.46 0.88 36.07 ? C8 ATP 601 A 1 HETATM 24 N N7 ATP . . . B 2 20.031 4.646 22.538 0.88 34.9 ? N7 ATP 601 A 1 HETATM 25 C C5 ATP . . . B 2 18.885 4.521 23.227 0.88 33.17 ? C5 ATP 601 A 1 HETATM 26 C C6 ATP . . . B 2 18.319 5.091 24.449 0.88 38.75 ? C6 ATP 601 A 1 HETATM 27 N N6 ATP . . . B 2 19.058 5.986 25.152 0.88 35.34 ? N6 ATP 601 A 1 HETATM 28 N N1 ATP . . . B 2 17.065 4.711 24.842 0.88 40.03 ? N1 ATP 601 A 1 HETATM 29 C C2 ATP . . . B 2 16.338 3.845 24.132 0.88 39.91 ? C2 ATP 601 A 1 HETATM 30 N N3 ATP . . . B 2 16.834 3.302 23 0.88 40.16 ? N3 ATP 601 A 1 HETATM 31 C C4 ATP . . . B 2 18.053 3.584 22.506 0.88 34.89 ? C4 ATP 601 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #