data_4ZCA # _model_server_result.job_id WJldbR8niOdMuPby_rczgQ _model_server_result.datetime_utc '2024-11-26 09:57:51' _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 4zca # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 4ZCA # _exptl.entry_id 4ZCA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 93.9 _cell.angle_gamma 90 _cell.entry_id 4ZCA _cell.length_a 52.54 _cell.length_b 77.83 _cell.length_c 93.12 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZCA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 1 A,B,C,D,E,F,G,H 3 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 C N N ? 2 E 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 OG1 THR 112 A THR 112 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc2 C O2B ADP . A ADP 601 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc3 D MG MG . A MG 602 1_555 G O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc4 D MG MG . A MG 602 1_555 G O HOH . A HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc5 D MG MG . A MG 602 1_555 G O HOH . A HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc6 D MG MG . A MG 602 1_555 G O HOH . A HOH 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc7 B OG1 THR 112 B THR 112 1_555 F MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc8 E O1B ADP . B ADP 601 1_555 F MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc9 E O3B ADP . B ADP 601 1_555 F MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc10 F MG MG . B MG 602 1_555 H O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc11 F MG MG . B MG 602 1_555 H O HOH . B HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc12 F MG MG . B MG 602 1_555 H O HOH . B HOH 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc13 F MG MG . B MG 602 1_555 H O HOH . B HOH 756 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? # _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 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 4ZCA _atom_sites.fract_transf_matrix[1][1] 0.019033 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001298 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012849 _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] 0.010764 _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 ADP A 1 601 601 ADP ADP . D 3 MG A 1 602 201 MG MG . E 2 ADP B 1 601 601 ADP ADP . F 3 MG B 1 602 202 MG MG . G 4 HOH A 1 701 70 HOH WAT . G 4 HOH A 2 702 10 HOH WAT . G 4 HOH A 3 703 24 HOH WAT . G 4 HOH A 4 704 35 HOH WAT . G 4 HOH A 5 705 112 HOH WAT . G 4 HOH A 6 706 51 HOH WAT . G 4 HOH A 7 707 30 HOH WAT . G 4 HOH A 8 708 73 HOH WAT . G 4 HOH A 9 709 42 HOH WAT . G 4 HOH A 10 710 88 HOH WAT . G 4 HOH A 11 711 50 HOH WAT . G 4 HOH A 12 712 9 HOH WAT . G 4 HOH A 13 713 105 HOH WAT . G 4 HOH A 14 714 86 HOH WAT . G 4 HOH A 15 715 18 HOH WAT . G 4 HOH A 16 716 14 HOH WAT . G 4 HOH A 17 717 123 HOH WAT . G 4 HOH A 18 718 100 HOH WAT . G 4 HOH A 19 719 5 HOH WAT . G 4 HOH A 20 720 94 HOH WAT . G 4 HOH A 21 721 104 HOH WAT . G 4 HOH A 22 722 81 HOH WAT . G 4 HOH A 23 723 75 HOH WAT . G 4 HOH A 24 724 108 HOH WAT . G 4 HOH A 25 725 65 HOH WAT . G 4 HOH A 26 726 15 HOH WAT . G 4 HOH A 27 727 125 HOH WAT . G 4 HOH A 28 728 107 HOH WAT . G 4 HOH A 29 729 127 HOH WAT . G 4 HOH A 30 730 25 HOH WAT . G 4 HOH A 31 731 46 HOH WAT . G 4 HOH A 32 732 56 HOH WAT . G 4 HOH A 33 733 22 HOH WAT . G 4 HOH A 34 734 19 HOH WAT . G 4 HOH A 35 735 13 HOH WAT . G 4 HOH A 36 736 110 HOH WAT . G 4 HOH A 37 737 85 HOH WAT . G 4 HOH A 38 738 78 HOH WAT . G 4 HOH A 39 739 137 HOH WAT . G 4 HOH A 40 740 59 HOH WAT . G 4 HOH A 41 741 106 HOH WAT . G 4 HOH A 42 742 135 HOH WAT . G 4 HOH A 43 743 11 HOH WAT . G 4 HOH A 44 744 124 HOH WAT . G 4 HOH A 45 745 36 HOH WAT . G 4 HOH A 46 746 97 HOH WAT . G 4 HOH A 47 747 21 HOH WAT . G 4 HOH A 48 748 27 HOH WAT . G 4 HOH A 49 749 55 HOH WAT . G 4 HOH A 50 750 69 HOH WAT . G 4 HOH A 51 751 90 HOH WAT . G 4 HOH A 52 752 140 HOH WAT . G 4 HOH A 53 753 89 HOH WAT . G 4 HOH A 54 754 117 HOH WAT . G 4 HOH A 55 755 33 HOH WAT . G 4 HOH A 56 756 80 HOH WAT . G 4 HOH A 57 757 12 HOH WAT . G 4 HOH A 58 758 92 HOH WAT . G 4 HOH A 59 759 113 HOH WAT . G 4 HOH A 60 760 98 HOH WAT . G 4 HOH A 61 761 53 HOH WAT . G 4 HOH A 62 762 131 HOH WAT . G 4 HOH A 63 763 39 HOH WAT . G 4 HOH A 64 764 43 HOH WAT . H 4 HOH B 1 701 54 HOH WAT . H 4 HOH B 2 702 4 HOH WAT . H 4 HOH B 3 703 74 HOH WAT . H 4 HOH B 4 704 1 HOH WAT . H 4 HOH B 5 705 17 HOH WAT . H 4 HOH B 6 706 49 HOH WAT . H 4 HOH B 7 707 16 HOH WAT . H 4 HOH B 8 708 32 HOH WAT . H 4 HOH B 9 709 38 HOH WAT . H 4 HOH B 10 710 121 HOH WAT . H 4 HOH B 11 711 91 HOH WAT . H 4 HOH B 12 712 109 HOH WAT . H 4 HOH B 13 713 23 HOH WAT . H 4 HOH B 14 714 119 HOH WAT . H 4 HOH B 15 715 41 HOH WAT . H 4 HOH B 16 716 31 HOH WAT . H 4 HOH B 17 717 103 HOH WAT . H 4 HOH B 18 718 126 HOH WAT . H 4 HOH B 19 719 76 HOH WAT . H 4 HOH B 20 720 102 HOH WAT . H 4 HOH B 21 721 139 HOH WAT . H 4 HOH B 22 722 138 HOH WAT . H 4 HOH B 23 723 118 HOH WAT . H 4 HOH B 24 724 2 HOH WAT . H 4 HOH B 25 725 133 HOH WAT . H 4 HOH B 26 726 77 HOH WAT . H 4 HOH B 27 727 99 HOH WAT . H 4 HOH B 28 728 93 HOH WAT . H 4 HOH B 29 729 34 HOH WAT . H 4 HOH B 30 730 62 HOH WAT . H 4 HOH B 31 731 40 HOH WAT . H 4 HOH B 32 732 44 HOH WAT . H 4 HOH B 33 733 67 HOH WAT . H 4 HOH B 34 734 95 HOH WAT . H 4 HOH B 35 735 45 HOH WAT . H 4 HOH B 36 736 83 HOH WAT . H 4 HOH B 37 737 48 HOH WAT . H 4 HOH B 38 738 52 HOH WAT . H 4 HOH B 39 739 129 HOH WAT . H 4 HOH B 40 740 57 HOH WAT . H 4 HOH B 41 741 37 HOH WAT . H 4 HOH B 42 742 96 HOH WAT . H 4 HOH B 43 743 79 HOH WAT . H 4 HOH B 44 744 66 HOH WAT . H 4 HOH B 45 745 116 HOH WAT . H 4 HOH B 46 746 8 HOH WAT . H 4 HOH B 47 747 130 HOH WAT . H 4 HOH B 48 748 28 HOH WAT . H 4 HOH B 49 749 122 HOH WAT . H 4 HOH B 50 750 136 HOH WAT . H 4 HOH B 51 751 58 HOH WAT . H 4 HOH B 52 752 120 HOH WAT . H 4 HOH B 53 753 26 HOH WAT . H 4 HOH B 54 754 111 HOH WAT . H 4 HOH B 55 755 132 HOH WAT . H 4 HOH B 56 756 3 HOH WAT . H 4 HOH B 57 757 134 HOH WAT . H 4 HOH B 58 758 6 HOH WAT . H 4 HOH B 59 759 68 HOH WAT . H 4 HOH B 60 760 82 HOH WAT . H 4 HOH B 61 761 61 HOH WAT . H 4 HOH B 62 762 47 HOH WAT . H 4 HOH B 63 763 101 HOH WAT . H 4 HOH B 64 764 115 HOH WAT . H 4 HOH B 65 765 63 HOH WAT . H 4 HOH B 66 766 72 HOH WAT . H 4 HOH B 67 767 71 HOH WAT . H 4 HOH B 68 768 128 HOH WAT . H 4 HOH B 69 769 20 HOH WAT . H 4 HOH B 70 770 114 HOH WAT . H 4 HOH B 71 771 29 HOH WAT . H 4 HOH B 72 772 84 HOH WAT . H 4 HOH B 73 773 64 HOH WAT . H 4 HOH B 74 774 87 HOH WAT . H 4 HOH B 75 775 60 HOH WAT . H 4 HOH B 76 776 7 HOH WAT . # 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 . . . E 2 47.198 45.14 -33.833 1 24.81 ? PB ADP 601 B 1 HETATM 2 O O1B ADP . . . E 2 47.626 44.697 -35.182 1 24.36 ? O1B ADP 601 B 1 HETATM 3 O O2B ADP . . . E 2 46.117 44.323 -33.235 1 20.72 ? O2B ADP 601 B 1 HETATM 4 O O3B ADP . . . E 2 47.015 46.604 -33.724 1 24.2 ? O3B ADP 601 B 1 HETATM 5 P PA ADP . . . E 2 49.945 45.241 -33.474 1 27.46 ? PA ADP 601 B 1 HETATM 6 O O1A ADP . . . E 2 50.317 44.256 -34.519 1 30.26 ? O1A ADP 601 B 1 HETATM 7 O O2A ADP . . . E 2 49.955 46.686 -33.818 1 23.72 ? O2A ADP 601 B 1 HETATM 8 O O3A ADP . . . E 2 48.483 44.842 -32.906 1 24.96 ? O3A ADP 601 B 1 HETATM 9 O O5' ADP . . . E 2 50.887 45.019 -32.184 1 30.27 ? O5' ADP 601 B 1 HETATM 10 C C5' ADP . . . E 2 52.283 45.248 -32.388 1 30.26 ? C5' ADP 601 B 1 HETATM 11 C C4' ADP . . . E 2 52.928 45.706 -31.08 1 29.16 ? C4' ADP 601 B 1 HETATM 12 O O4' ADP . . . E 2 52.86 44.594 -30.172 1 27.98 ? O4' ADP 601 B 1 HETATM 13 C C3' ADP . . . E 2 54.411 45.838 -31.369 1 31.98 ? C3' ADP 601 B 1 HETATM 14 O O3' ADP . . . E 2 55.087 46.186 -30.152 1 33.43 ? O3' ADP 601 B 1 HETATM 15 C C2' ADP . . . E 2 54.647 44.376 -31.697 1 31.37 ? C2' ADP 601 B 1 HETATM 16 O O2' ADP . . . E 2 56.053 44.092 -31.734 1 37.37 ? O2' ADP 601 B 1 HETATM 17 C C1' ADP . . . E 2 54.011 43.776 -30.453 1 26.5 ? C1' ADP 601 B 1 HETATM 18 N N9 ADP . . . E 2 53.698 42.339 -30.607 1 27.22 ? N9 ADP 601 B 1 HETATM 19 C C8 ADP . . . E 2 52.498 41.795 -30.798 1 26.5 ? C8 ADP 601 B 1 HETATM 20 N N7 ADP . . . E 2 52.658 40.476 -30.849 1 25.13 ? N7 ADP 601 B 1 HETATM 21 C C5 ADP . . . E 2 53.953 40.209 -30.684 1 26.6 ? C5 ADP 601 B 1 HETATM 22 C C6 ADP . . . E 2 54.6 39.049 -30.583 1 26.69 ? C6 ADP 601 B 1 HETATM 23 N N6 ADP . . . E 2 53.887 37.949 -30.769 1 25.69 ? N6 ADP 601 B 1 HETATM 24 N N1 ADP . . . E 2 55.927 39.006 -30.383 1 27.59 ? N1 ADP 601 B 1 HETATM 25 C C2 ADP . . . E 2 56.642 40.203 -30.297 1 26.34 ? C2 ADP 601 B 1 HETATM 26 N N3 ADP . . . E 2 55.929 41.4 -30.402 1 27.31 ? N3 ADP 601 B 1 HETATM 27 C C4 ADP . . . E 2 54.594 41.359 -30.578 1 26.7 ? C4 ADP 601 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #