data_4TSF # _model_server_result.job_id TNTSlJWuOXuJxGkATMlA9A _model_server_result.datetime_utc '2024-11-28 03:22:58' _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 4tsf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":600}' # _entry.id 4TSF # _exptl.entry_id 4TSF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 7 _entity.src_method nat _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 90 _cell.angle_gamma 90 _cell.entry_id 4TSF _cell.length_a 108.015 _cell.length_b 154.42 _cell.length_c 269.465 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TSF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details Nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 P N N ? 7 R 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 176 A THR 176 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc2 J O2G ATP . A ATP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc3 J O2B ATP . A ATP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc4 K MG MG . A MG 601 1_555 T O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc5 K MG MG . A MG 601 1_555 T O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 K MG MG . A MG 601 1_555 T O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc7 B OG1 THR 176 B THR 176 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc8 L O2G ATP . B ATP 600 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc9 L O3G ATP . B ATP 600 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? metalc ? metalc10 L O2B ATP . B ATP 600 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc11 M MG MG . B MG 601 1_555 U O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc12 M MG MG . B MG 601 1_555 U O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc13 M MG MG . B MG 601 1_555 U O HOH . B HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc14 C OG1 THR 176 C THR 176 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc15 N O2G ATP . C ATP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc16 N O2B ATP . C ATP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc17 O MG MG . C MG 601 1_555 V O HOH . C HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc18 O MG MG . C MG 601 1_555 V O HOH . C HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc19 O MG MG . C MG 601 1_555 V O HOH . C HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc20 D OG1 THR 165 D THR 163 1_555 Q MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc21 P O2B ADP . D ADP 600 1_555 Q MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc22 Q MG MG . D MG 601 1_555 W O HOH . D HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc23 Q MG MG . D MG 601 1_555 W O HOH . D HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc24 Q MG MG . D MG 601 1_555 W O HOH . D HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc25 Q MG MG . D MG 601 1_555 W O HOH . D HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc26 F OG1 THR 165 F THR 163 1_555 S MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc27 R O2B ADP . F ADP 600 1_555 S MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc28 R O3B ADP . F ADP 600 1_555 S MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc29 S MG MG . F MG 601 1_555 X O HOH . F HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc30 S MG MG . F MG 601 1_555 X O HOH . F HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc31 S MG MG . F MG 601 1_555 X O HOH . F HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc32 S MG MG . F MG 601 1_555 X O HOH . F HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? # _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 4TSF _atom_sites.fract_transf_matrix[1][1] 0.009258 _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] 0.006476 _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] 0.003711 _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 J 5 ATP A 1 600 600 ATP ATP . K 6 MG A 1 601 601 MG MO6 . L 5 ATP B 1 600 600 ATP ATP . M 6 MG B 1 601 601 MG MO6 . N 5 ATP C 1 600 600 ATP ATP . O 6 MG C 1 601 601 MG MO6 . P 7 ADP D 1 600 600 ADP ADP . Q 6 MG D 1 601 601 MG MO6 . R 7 ADP F 1 600 600 ADP ADP . S 6 MG F 1 601 601 MG MO6 . T 8 HOH A 1 701 601 HOH MO6 . T 8 HOH A 2 702 601 HOH MO6 . T 8 HOH A 3 703 601 HOH MO6 . U 8 HOH B 1 701 601 HOH MO6 . U 8 HOH B 2 702 601 HOH MO6 . U 8 HOH B 3 703 601 HOH MO6 . V 8 HOH C 1 701 601 HOH MO6 . V 8 HOH C 2 702 601 HOH MO6 . V 8 HOH C 3 703 601 HOH MO6 . W 8 HOH D 1 701 601 HOH MO6 . W 8 HOH D 2 702 601 HOH MO6 . W 8 HOH D 3 703 601 HOH MO6 . W 8 HOH D 4 704 601 HOH MO6 . X 8 HOH F 1 701 601 HOH MO6 . X 8 HOH F 2 702 601 HOH MO6 . X 8 HOH F 3 703 601 HOH MO6 . X 8 HOH F 4 704 601 HOH MO6 . # 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 . . . R 7 60.047 -3.584 -37.053 1 60.49 ? PB ADP 600 F 1 HETATM 2 O O1B ADP . . . R 7 58.542 -3.54 -37.15 1 60.35 ? O1B ADP 600 F 1 HETATM 3 O O2B ADP . . . R 7 60.7 -2.255 -36.76 1 60.81 ? O2B ADP 600 F 1 HETATM 4 O O3B ADP . . . R 7 60.577 -4.729 -36.224 1 60.99 ? O3B ADP 600 F 1 HETATM 5 P PA ADP . . . R 7 62.019 -3.88 -39.051 1 60.79 ? PA ADP 600 F 1 HETATM 6 O O1A ADP . . . R 7 62.349 -2.434 -39.327 1 61.25 ? O1A ADP 600 F 1 HETATM 7 O O2A ADP . . . R 7 62.879 -4.676 -38.1 1 60.69 ? O2A ADP 600 F 1 HETATM 8 O O3A ADP . . . R 7 60.487 -3.95 -38.56 1 60.77 ? O3A ADP 600 F 1 HETATM 9 O O5' ADP . . . R 7 61.959 -4.677 -40.449 1 61.62 ? O5' ADP 600 F 1 HETATM 10 C C5' ADP . . . R 7 61.617 -6.061 -40.455 1 62.68 ? C5' ADP 600 F 1 HETATM 11 C C4' ADP . . . R 7 61.709 -6.657 -41.857 1 63.46 ? C4' ADP 600 F 1 HETATM 12 O O4' ADP . . . R 7 60.932 -5.911 -42.801 1 64.15 ? O4' ADP 600 F 1 HETATM 13 C C3' ADP . . . R 7 63.129 -6.693 -42.401 1 63.53 ? C3' ADP 600 F 1 HETATM 14 O O3' ADP . . . R 7 63.773 -7.933 -42.096 1 63.92 ? O3' ADP 600 F 1 HETATM 15 C C2' ADP . . . R 7 62.964 -6.496 -43.894 1 63.98 ? C2' ADP 600 F 1 HETATM 16 O O2' ADP . . . R 7 63.005 -7.746 -44.59 1 63.81 ? O2' ADP 600 F 1 HETATM 17 C C1' ADP . . . R 7 61.596 -5.852 -44.07 1 64.45 ? C1' ADP 600 F 1 HETATM 18 N N9 ADP . . . R 7 61.757 -4.444 -44.521 1 65.24 ? N9 ADP 600 F 1 HETATM 19 C C8 ADP . . . R 7 61.596 -3.347 -43.756 1 65.71 ? C8 ADP 600 F 1 HETATM 20 N N7 ADP . . . R 7 61.821 -2.217 -44.474 1 66.08 ? N7 ADP 600 F 1 HETATM 21 C C5 ADP . . . R 7 62.136 -2.586 -45.726 1 65.74 ? C5 ADP 600 F 1 HETATM 22 C C6 ADP . . . R 7 62.49 -1.892 -46.987 1 65.72 ? C6 ADP 600 F 1 HETATM 23 N N6 ADP . . . R 7 62.55 -0.54 -47.047 1 65.79 ? N6 ADP 600 F 1 HETATM 24 N N1 ADP . . . R 7 62.747 -2.657 -48.075 1 66.27 ? N1 ADP 600 F 1 HETATM 25 C C2 ADP . . . R 7 62.691 -4.006 -48.036 1 66.25 ? C2 ADP 600 F 1 HETATM 26 N N3 ADP . . . R 7 62.376 -4.694 -46.919 1 65.98 ? N3 ADP 600 F 1 HETATM 27 C C4 ADP . . . R 7 62.094 -4.056 -45.755 1 65.72 ? C4 ADP 600 F 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #