data_3VH4 # _model_server_result.job_id s5KXLNAbWrkJrKBMyPGZIg _model_server_result.datetime_utc '2024-10-12 10:21:49' _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 3vh4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":702}' # _entry.id 3VH4 # _exptl.entry_id 3VH4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _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 3VH4 _cell.length_a 69.282 _cell.length_b 69.282 _cell.length_c 219.605 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VH4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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 # 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' 7_465 y-1,x+1,-z 0 1 0 1 0 0 0 0 -1 -69.282 69.282 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 OD2 ASP 148 A ASP 438 1_555 E MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc2 A SG CYS 195 A CYS 485 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc3 A SG CYS 198 A CYS 488 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc4 A SG CYS 279 A CYS 569 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc5 A SG CYS 282 A CYS 572 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc6 D O2B ATP . A ATP 702 1_555 E MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc7 D O2A ATP . A ATP 702 1_555 E MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc8 D O3G ATP . A ATP 702 1_555 E MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? # _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 3VH4 _atom_sites.fract_transf_matrix[1][1] 0.014434 _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] 0.014434 _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] 0.004554 _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 ZN A 1 701 701 ZN ZN2 . D 4 ATP A 1 702 702 ATP ATP . E 5 MG A 1 703 703 MG MG2 . # 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 . . . D 4 -47.289 18.301 15.874 0.65 91.38 ? PG ATP 702 A 1 HETATM 2 O O1G ATP . . . D 4 -47.882 18.982 17.054 0.65 90.06 ? O1G ATP 702 A 1 HETATM 3 O O2G ATP . . . D 4 -48.168 18.657 14.567 0.65 92.21 ? O2G ATP 702 A 1 HETATM 4 O O3G ATP . . . D 4 -45.773 18.819 15.643 0.65 90.52 ? O3G ATP 702 A 1 HETATM 5 P PB ATP . . . D 4 -46.415 15.863 15.078 0.65 86.28 ? PB ATP 702 A 1 HETATM 6 O O1B ATP . . . D 4 -47.124 14.626 14.717 0.65 85.42 ? O1B ATP 702 A 1 HETATM 7 O O2B ATP . . . D 4 -44.97 15.492 15.723 0.65 85.7 ? O2B ATP 702 A 1 HETATM 8 O O3B ATP . . . D 4 -47.314 16.689 16.157 0.65 88.6 ? O3B ATP 702 A 1 HETATM 9 P PA ATP . . . D 4 -44.674 16.977 13.203 0.65 80.1 ? PA ATP 702 A 1 HETATM 10 O O1A ATP . . . D 4 -44.698 18.074 12.215 0.65 79.71 ? O1A ATP 702 A 1 HETATM 11 O O2A ATP . . . D 4 -43.711 17.403 14.427 0.65 79.76 ? O2A ATP 702 A 1 HETATM 12 O O3A ATP . . . D 4 -46.226 16.731 13.696 0.65 84.4 ? O3A ATP 702 A 1 HETATM 13 O O5' ATP . . . D 4 -44.101 15.69 12.414 0.65 79.17 ? O5' ATP 702 A 1 HETATM 14 C C5' ATP . . . D 4 -42.95 15.159 13.059 0.65 75.77 ? C5' ATP 702 A 1 HETATM 15 C C4' ATP . . . D 4 -42.986 13.655 12.837 0.65 74.71 ? C4' ATP 702 A 1 HETATM 16 O O4' ATP . . . D 4 -41.78 12.992 13.324 0.65 75.11 ? O4' ATP 702 A 1 HETATM 17 C C3' ATP . . . D 4 -44.191 13.04 13.573 0.65 73.96 ? C3' ATP 702 A 1 HETATM 18 O O3' ATP . . . D 4 -45.062 12.412 12.634 0.65 72.67 ? O3' ATP 702 A 1 HETATM 19 C C2' ATP . . . D 4 -43.555 12.06 14.578 0.65 74.7 ? C2' ATP 702 A 1 HETATM 20 O O2' ATP . . . D 4 -44.411 10.923 14.835 0.65 71.4 ? O2' ATP 702 A 1 HETATM 21 C C1' ATP . . . D 4 -42.197 11.725 13.903 0.65 74.5 ? C1' ATP 702 A 1 HETATM 22 N N9 ATP . . . D 4 -41.198 11.318 14.882 0.65 75.31 ? N9 ATP 702 A 1 HETATM 23 C C8 ATP . . . D 4 -40.661 12.11 15.875 0.65 75.66 ? C8 ATP 702 A 1 HETATM 24 N N7 ATP . . . D 4 -39.786 11.428 16.57 0.65 76.86 ? N7 ATP 702 A 1 HETATM 25 C C5 ATP . . . D 4 -39.701 10.169 16.073 0.65 77.04 ? C5 ATP 702 A 1 HETATM 26 C C6 ATP . . . D 4 -38.94 9 16.402 0.65 76.05 ? C6 ATP 702 A 1 HETATM 27 N N6 ATP . . . D 4 -38.051 9.026 17.453 0.65 74.66 ? N6 ATP 702 A 1 HETATM 28 N N1 ATP . . . D 4 -39.112 7.873 15.66 0.65 75.95 ? N1 ATP 702 A 1 HETATM 29 C C2 ATP . . . D 4 -39.976 7.832 14.63 0.65 75.67 ? C2 ATP 702 A 1 HETATM 30 N N3 ATP . . . D 4 -40.712 8.904 14.293 0.65 75.93 ? N3 ATP 702 A 1 HETATM 31 C C4 ATP . . . D 4 -40.602 10.079 14.976 0.65 76.39 ? C4 ATP 702 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #