data_6DE3 # _model_server_result.job_id yuEONVdjWolpCvzSB11BMw _model_server_result.datetime_utc '2024-11-15 02:51:21' _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 6de3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":602}' # _entry.id 6DE3 # _exptl.entry_id 6DE3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 6DE3 _cell.length_a 92.362 _cell.length_b 129.098 _cell.length_c 131.016 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DE3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 129.098 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 129.098 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 C O1G ATP . A ATP 602 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc2 C O1B ATP . A ATP 602 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc3 C O3B ATP . A ATP 602 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc4 C O1G ATP . A ATP 602 1_555 D MG MG . A MG 603 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc5 C O1B ATP . A ATP 602 1_555 D MG MG . A MG 603 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc6 C O3B ATP . A ATP 602 1_555 D MG MG . A MG 603 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.98 ? # _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 6DE3 _atom_sites.fract_transf_matrix[1][1] 0.010827 _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] 0.007746 _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] 0.007633 _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 PO4 A 1 601 601 PO4 PO4 . C 3 ATP A 1 602 602 ATP ATP . D 4 MG A 1 603 603 MG MG . E 5 HOH A 1 701 10 HOH HOH . E 5 HOH A 2 702 2 HOH HOH . E 5 HOH A 3 703 22 HOH HOH . E 5 HOH A 4 704 11 HOH HOH . E 5 HOH A 5 705 3 HOH HOH . E 5 HOH A 6 706 1 HOH HOH . E 5 HOH A 7 707 24 HOH HOH . E 5 HOH A 8 708 12 HOH HOH . E 5 HOH A 9 709 37 HOH HOH . E 5 HOH A 10 710 32 HOH HOH . E 5 HOH A 11 711 39 HOH HOH . E 5 HOH A 12 712 14 HOH HOH . E 5 HOH A 13 713 4 HOH HOH . E 5 HOH A 14 714 36 HOH HOH . E 5 HOH A 15 715 35 HOH HOH . E 5 HOH A 16 716 38 HOH HOH . E 5 HOH A 17 717 42 HOH HOH . E 5 HOH A 18 718 7 HOH HOH . E 5 HOH A 19 719 8 HOH HOH . E 5 HOH A 20 720 27 HOH HOH . E 5 HOH A 21 721 41 HOH HOH . E 5 HOH A 22 722 16 HOH HOH . E 5 HOH A 23 723 23 HOH HOH . E 5 HOH A 24 724 6 HOH HOH . E 5 HOH A 25 725 40 HOH HOH . E 5 HOH A 26 726 45 HOH HOH . E 5 HOH A 27 727 26 HOH HOH . E 5 HOH A 28 728 33 HOH HOH . E 5 HOH A 29 729 20 HOH HOH . E 5 HOH A 30 730 21 HOH HOH . E 5 HOH A 31 731 18 HOH HOH . E 5 HOH A 32 732 9 HOH HOH . E 5 HOH A 33 733 5 HOH HOH . E 5 HOH A 34 734 48 HOH HOH . E 5 HOH A 35 735 29 HOH HOH . E 5 HOH A 36 736 19 HOH HOH . E 5 HOH A 37 737 44 HOH HOH . E 5 HOH A 38 738 30 HOH HOH . E 5 HOH A 39 739 43 HOH HOH . E 5 HOH A 40 740 49 HOH HOH . E 5 HOH A 41 741 25 HOH HOH . E 5 HOH A 42 742 28 HOH HOH . E 5 HOH A 43 743 34 HOH HOH . E 5 HOH A 44 744 15 HOH HOH . E 5 HOH A 45 745 17 HOH HOH . E 5 HOH A 46 746 47 HOH HOH . E 5 HOH A 47 747 31 HOH HOH . E 5 HOH A 48 748 50 HOH HOH . E 5 HOH A 49 749 46 HOH HOH . E 5 HOH A 50 750 13 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 . . . C 3 -2.588 41.301 1.116 1 46.28 ? PG ATP 602 A 1 HETATM 2 O O1G ATP . . . C 3 -1.54 41.019 0.064 1 51.19 ? O1G ATP 602 A 1 HETATM 3 O O2G ATP . . . C 3 -2.137 41.111 2.545 1 37.77 ? O2G ATP 602 A 1 HETATM 4 O O3G ATP . . . C 3 -3.946 40.739 0.806 1 27.89 ? O3G ATP 602 A 1 HETATM 5 P PB ATP . . . C 3 -2.097 44.007 1.893 1 52.57 ? PB ATP 602 A 1 HETATM 6 O O1B ATP . . . C 3 -0.631 44.015 1.489 1 50.2 ? O1B ATP 602 A 1 HETATM 7 O O2B ATP . . . C 3 -2.448 43.739 3.32 1 57.91 ? O2B ATP 602 A 1 HETATM 8 O O3B ATP . . . C 3 -2.81 42.89 0.977 1 56.72 ? O3B ATP 602 A 1 HETATM 9 P PA ATP . . . C 3 -4.409 45.755 1.639 1 56.54 ? PA ATP 602 A 1 HETATM 10 O O1A ATP . . . C 3 -4.825 46.868 0.693 1 39.93 ? O1A ATP 602 A 1 HETATM 11 O O2A ATP . . . C 3 -5.234 44.496 1.676 1 64.01 ? O2A ATP 602 A 1 HETATM 12 O O3A ATP . . . C 3 -2.846 45.357 1.381 1 57.36 ? O3A ATP 602 A 1 HETATM 13 O O5' ATP . . . C 3 -4.421 46.361 3.109 1 51.86 ? O5' ATP 602 A 1 HETATM 14 C C5' ATP . . . C 3 -4.642 47.748 3.262 1 48.56 ? C5' ATP 602 A 1 HETATM 15 C C4' ATP . . . C 3 -3.613 48.344 4.224 1 41.25 ? C4' ATP 602 A 1 HETATM 16 O O4' ATP . . . C 3 -3.633 47.709 5.505 1 36.36 ? O4' ATP 602 A 1 HETATM 17 C C3' ATP . . . C 3 -2.189 48.243 3.7 1 28.78 ? C3' ATP 602 A 1 HETATM 18 O O3' ATP . . . C 3 -1.629 49.545 3.86 1 35.84 ? O3' ATP 602 A 1 HETATM 19 C C2' ATP . . . C 3 -1.479 47.282 4.62 1 24.2 ? C2' ATP 602 A 1 HETATM 20 O O2' ATP . . . C 3 -0.133 47.669 4.892 1 29.85 ? O2' ATP 602 A 1 HETATM 21 C C1' ATP . . . C 3 -2.281 47.434 5.886 1 35.97 ? C1' ATP 602 A 1 HETATM 22 N N9 ATP . . . C 3 -2.257 46.209 6.705 1 45.58 ? N9 ATP 602 A 1 HETATM 23 C C8 ATP . . . C 3 -2.113 44.943 6.278 1 46.04 ? C8 ATP 602 A 1 HETATM 24 N N7 ATP . . . C 3 -2.156 44.087 7.326 1 44.68 ? N7 ATP 602 A 1 HETATM 25 C C5 ATP . . . C 3 -2.331 44.82 8.439 1 47.3 ? C5 ATP 602 A 1 HETATM 26 C C6 ATP . . . C 3 -2.461 44.554 9.88 1 47.09 ? C6 ATP 602 A 1 HETATM 27 N N6 ATP . . . C 3 -2.412 43.288 10.346 1 49.9 ? N6 ATP 602 A 1 HETATM 28 N N1 ATP . . . C 3 -2.628 45.61 10.706 1 49.21 ? N1 ATP 602 A 1 HETATM 29 C C2 ATP . . . C 3 -2.676 46.872 10.243 1 51.08 ? C2 ATP 602 A 1 HETATM 30 N N3 ATP . . . C 3 -2.556 47.192 8.947 1 48.67 ? N3 ATP 602 A 1 HETATM 31 C C4 ATP . . . C 3 -2.385 46.222 8.023 1 48.99 ? C4 ATP 602 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 428 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #