data_3VNU # _model_server_result.job_id 9EHhXcf9fk5qewSBx0Ut3w _model_server_result.datetime_utc '2024-11-15 05:28:52' _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 3vnu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2501}' # _entry.id 3VNU # _exptl.entry_id 3VNU _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 3VNU _cell.length_a 139.005 _cell.length_b 255.506 _cell.length_c 101.425 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VNU _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 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 OD1 ASP 968 A ASP 968 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc2 A OD1 ASP 968 A ASP 968 1_555 F CA CA . A CA 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc3 A O LEU 969 A LEU 969 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc4 A OD2 ASP 1053 A ASP 1053 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc5 A OD1 ASP 1053 A ASP 1053 1_555 F CA CA . A CA 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc6 D O2A ATP . A ATP 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc7 D O2B ATP . A ATP 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc8 D O2G ATP . A ATP 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.985 ? metalc ? metalc9 D O3B ATP . A ATP 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.176 ? hydrog WATSON-CRICK hydrog1 B N3 C 3 G C 2003 1_555 C N1 G 6 T G 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 C 3 G C 2003 1_555 C O6 G 6 T G 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 C 3 G C 2003 1_555 C N2 G 6 T G 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 U 4 G U 2004 1_555 C N1 A 5 T A 2105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 U 4 G U 2004 1_555 C N6 A 5 T A 2105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog6 B N6 A 5 G A 2005 1_555 C O2 U 4 T U 2104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog7 B O2 C 6 G C 2006 1_555 C N1 G 3 T G 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog8 B O2 C 7 G C 2007 1_555 C N1 G 2 T G 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 C 8 G C 2008 1_555 C N1 G 1 T G 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 C 8 G C 2008 1_555 C O6 G 1 T G 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 C 8 G C 2008 1_555 C N2 G 1 T G 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 109 n n PG O2G ATP sing 110 n n PG O3G ATP sing 111 n n PG O3B ATP sing 112 n n O2G HOG2 ATP sing 113 n n O3G HOG3 ATP sing 114 n n PB O1B ATP doub 115 n n PB O2B ATP sing 116 n n PB O3B ATP sing 117 n n PB O3A ATP sing 118 n n O2B HOB2 ATP sing 119 n n PA O1A ATP doub 120 n n PA O2A ATP sing 121 n n PA O3A ATP sing 122 n n PA O5' ATP sing 123 n n O2A HOA2 ATP sing 124 n n O5' C5' ATP sing 125 n n C5' C4' ATP sing 126 n n C5' "H5'1" ATP sing 127 n n C5' "H5'2" ATP sing 128 n n C4' O4' ATP sing 129 n n C4' C3' ATP sing 130 n n C4' H4' ATP sing 131 n n O4' C1' ATP sing 132 n n C3' O3' ATP sing 133 n n C3' C2' ATP sing 134 n n C3' H3' ATP sing 135 n n O3' HO3' ATP sing 136 n n C2' O2' ATP sing 137 n n C2' C1' ATP sing 138 n n C2' H2' ATP sing 139 n n O2' HO2' ATP sing 140 n n C1' N9 ATP sing 141 n n C1' H1' ATP sing 142 n n N9 C8 ATP sing 143 n y N9 C4 ATP sing 144 n y C8 N7 ATP doub 145 n y C8 H8 ATP sing 146 n n N7 C5 ATP sing 147 n y C5 C6 ATP sing 148 n y C5 C4 ATP doub 149 n y C6 N6 ATP sing 150 n n C6 N1 ATP doub 151 n y N6 HN61 ATP sing 152 n n N6 HN62 ATP sing 153 n n N1 C2 ATP sing 154 n y C2 N3 ATP doub 155 n y C2 H2 ATP sing 156 n n N3 C4 ATP sing 157 n y # _atom_sites.entry_id 3VNU _atom_sites.fract_transf_matrix[1][1] 0.007194 _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] 0.003914 _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] 0.00986 _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 D 4 ATP A 1 2501 2501 ATP ATP . E 5 CA A 1 2502 3001 CA CA . F 5 CA A 1 2503 3002 CA CA . G 6 HOH A 1 3101 3101 HOH HOH . G 6 HOH A 2 3102 3102 HOH HOH . G 6 HOH A 3 3103 3103 HOH HOH . G 6 HOH A 4 3104 3104 HOH HOH . G 6 HOH A 5 3105 3105 HOH HOH . G 6 HOH A 6 3106 3106 HOH HOH . G 6 HOH A 7 3107 3107 HOH HOH . G 6 HOH A 8 3108 3108 HOH HOH . G 6 HOH A 9 3109 3109 HOH HOH . G 6 HOH A 10 3110 3111 HOH HOH . G 6 HOH A 11 3111 3110 HOH HOH . H 6 HOH T 1 2201 3112 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 . . . D 4 17.429 71.441 -2.317 1 78.88 ? PG ATP 2501 A 1 HETATM 2 O O1G ATP . . . D 4 18.265 70.561 -1.419 1 75.37 ? O1G ATP 2501 A 1 HETATM 3 O O2G ATP . . . D 4 17.851 71.475 -3.773 1 83.54 ? O2G ATP 2501 A 1 HETATM 4 O O3G ATP . . . D 4 17.212 72.819 -1.741 1 79.3 ? O3G ATP 2501 A 1 HETATM 5 P PB ATP . . . D 4 15.649 69.247 -1.895 1 65.44 ? PB ATP 2501 A 1 HETATM 6 O O1B ATP . . . D 4 14.9 69.219 -0.628 1 67.8 ? O1B ATP 2501 A 1 HETATM 7 O O2B ATP . . . D 4 14.963 68.521 -3.013 1 70.82 ? O2B ATP 2501 A 1 HETATM 8 O O3B ATP . . . D 4 15.946 70.786 -2.301 1 72.86 ? O3B ATP 2501 A 1 HETATM 9 P PA ATP . . . D 4 17.741 67.456 -2.304 1 66.66 ? PA ATP 2501 A 1 HETATM 10 O O1A ATP . . . D 4 19.067 67.138 -1.691 1 69.91 ? O1A ATP 2501 A 1 HETATM 11 O O2A ATP . . . D 4 17.658 67.884 -3.749 1 64.26 ? O2A ATP 2501 A 1 HETATM 12 O O3A ATP . . . D 4 17.015 68.563 -1.392 1 64.34 ? O3A ATP 2501 A 1 HETATM 13 O O5' ATP . . . D 4 16.982 66.086 -2.102 1 63.4 ? O5' ATP 2501 A 1 HETATM 14 C C5' ATP . . . D 4 16.472 65.354 -3.185 1 66.14 ? C5' ATP 2501 A 1 HETATM 15 C C4' ATP . . . D 4 15.502 64.472 -2.458 1 76.72 ? C4' ATP 2501 A 1 HETATM 16 O O4' ATP . . . D 4 16.21 63.784 -1.426 1 84.18 ? O4' ATP 2501 A 1 HETATM 17 C C3' ATP . . . D 4 14.416 65.255 -1.727 1 86.08 ? C3' ATP 2501 A 1 HETATM 18 O O3' ATP . . . D 4 13.213 65.459 -2.466 1 96.21 ? O3' ATP 2501 A 1 HETATM 19 C C2' ATP . . . D 4 14.077 64.374 -0.548 1 96.87 ? C2' ATP 2501 A 1 HETATM 20 O O2' ATP . . . D 4 12.875 63.621 -0.795 1 105.31 ? O2' ATP 2501 A 1 HETATM 21 C C1' ATP . . . D 4 15.255 63.416 -0.411 1 96.16 ? C1' ATP 2501 A 1 HETATM 22 N N9 ATP . . . D 4 15.784 63.432 0.994 1 93.75 ? N9 ATP 2501 A 1 HETATM 23 C C8 ATP . . . D 4 17.027 63.803 1.352 1 87.83 ? C8 ATP 2501 A 1 HETATM 24 N N7 ATP . . . D 4 17.194 63.706 2.702 1 82.91 ? N7 ATP 2501 A 1 HETATM 25 C C5 ATP . . . D 4 16.026 63.273 3.239 1 85.65 ? C5 ATP 2501 A 1 HETATM 26 C C6 ATP . . . D 4 15.482 62.945 4.598 1 83.37 ? C6 ATP 2501 A 1 HETATM 27 N N6 ATP . . . D 4 16.229 63.057 5.72 1 78.92 ? N6 ATP 2501 A 1 HETATM 28 N N1 ATP . . . D 4 14.199 62.514 4.696 1 83.34 ? N1 ATP 2501 A 1 HETATM 29 C C2 ATP . . . D 4 13.405 62.379 3.611 1 85.23 ? C2 ATP 2501 A 1 HETATM 30 N N3 ATP . . . D 4 13.826 62.65 2.36 1 83.94 ? N3 ATP 2501 A 1 HETATM 31 C C4 ATP . . . D 4 15.096 63.093 2.106 1 88.21 ? C4 ATP 2501 A 1 # _model_server_stats.io_time_ms 88 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #