data_4USJ # _model_server_result.job_id 2AL9Ofzph1Ttb8qqzw59KA _model_server_result.datetime_utc '2024-12-21 13:10:42' _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 4usj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 4USJ # _exptl.entry_id 4USJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 4USJ _cell.length_a 171.43 _cell.length_b 171.43 _cell.length_c 171.43 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4USJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _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 F O2B ADP . A ADP 302 1_555 H MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc2 F O1A ADP . A ADP 302 1_555 H MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc3 H MG MG . A MG 304 1_555 Q O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc4 H MG MG . A MG 304 1_555 Q O HOH . A HOH 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc5 H MG MG . A MG 304 1_555 Q O HOH . A HOH 2031 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc6 C O GLY 54 C GLY 54 1_555 L MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc7 K O1G ATP . C ATP 301 1_555 L MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc8 K O2B ATP . C ATP 301 1_555 L MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc9 K O2A ATP . C ATP 301 1_555 L MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc10 L MG MG . C MG 302 1_555 S O HOH . C HOH 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc11 L MG MG . C MG 302 1_555 S O HOH . C HOH 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc12 D O GLY 54 D GLY 54 1_555 O MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc13 N O2A ATP . D ATP 301 1_555 O MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc14 N O2B ATP . D ATP 301 1_555 O MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc15 N O1G ATP . D ATP 301 1_555 O MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc16 O MG MG . D MG 302 1_555 T O HOH . D HOH 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc17 O MG MG . D MG 302 1_555 T O HOH . D HOH 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? # _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 4USJ _atom_sites.fract_transf_matrix[1][1] 0.005833 _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] 0.005833 _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] 0.005833 _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 E 3 ARG A 1 301 301 ARG ARG . F 4 ADP A 1 302 302 ADP ADP . G 5 NLG A 1 303 303 NLG NLG . H 6 MG A 1 304 304 MG MG . I 3 ARG B 1 301 301 ARG ARG . J 7 X2W B 1 303 303 X2W X2W . K 8 ATP C 1 301 301 ATP ATP . L 6 MG C 1 302 302 MG MG . M 9 GLN C 1 303 303 GLN GLN . N 8 ATP D 1 301 301 ATP ATP . O 6 MG D 1 302 302 MG MG . P 9 GLN D 1 303 303 GLN GLN . Q 10 HOH A 1 2001 2001 HOH HOH . Q 10 HOH A 2 2002 2002 HOH HOH . Q 10 HOH A 3 2003 2003 HOH HOH . Q 10 HOH A 4 2004 2004 HOH HOH . Q 10 HOH A 5 2005 2005 HOH HOH . Q 10 HOH A 6 2006 2006 HOH HOH . Q 10 HOH A 7 2007 2007 HOH HOH . Q 10 HOH A 8 2008 2008 HOH HOH . Q 10 HOH A 9 2009 2009 HOH HOH . Q 10 HOH A 10 2010 2010 HOH HOH . Q 10 HOH A 11 2011 2011 HOH HOH . Q 10 HOH A 12 2012 2012 HOH HOH . Q 10 HOH A 13 2013 2013 HOH HOH . Q 10 HOH A 14 2014 2014 HOH HOH . Q 10 HOH A 15 2015 2015 HOH HOH . Q 10 HOH A 16 2016 2016 HOH HOH . Q 10 HOH A 17 2017 2017 HOH HOH . Q 10 HOH A 18 2018 2018 HOH HOH . Q 10 HOH A 19 2019 2019 HOH HOH . Q 10 HOH A 20 2020 2020 HOH HOH . Q 10 HOH A 21 2021 2021 HOH HOH . Q 10 HOH A 22 2022 2022 HOH HOH . Q 10 HOH A 23 2023 2023 HOH HOH . Q 10 HOH A 24 2024 2024 HOH HOH . Q 10 HOH A 25 2025 2025 HOH HOH . Q 10 HOH A 26 2026 2026 HOH HOH . Q 10 HOH A 27 2027 2027 HOH HOH . Q 10 HOH A 28 2028 2028 HOH HOH . Q 10 HOH A 29 2029 2029 HOH HOH . Q 10 HOH A 30 2030 2030 HOH HOH . Q 10 HOH A 31 2031 2031 HOH HOH . Q 10 HOH A 32 2032 2032 HOH HOH . Q 10 HOH A 33 2033 2033 HOH HOH . Q 10 HOH A 34 2034 2034 HOH HOH . Q 10 HOH A 35 2035 2035 HOH HOH . Q 10 HOH A 36 2036 2036 HOH HOH . Q 10 HOH A 37 2037 2037 HOH HOH . R 10 HOH B 1 2001 2001 HOH HOH . R 10 HOH B 2 2002 2002 HOH HOH . R 10 HOH B 3 2003 2003 HOH HOH . R 10 HOH B 4 2004 2004 HOH HOH . R 10 HOH B 5 2005 2005 HOH HOH . R 10 HOH B 6 2006 2006 HOH HOH . R 10 HOH B 7 2007 2007 HOH HOH . R 10 HOH B 8 2008 2008 HOH HOH . R 10 HOH B 9 2009 2009 HOH HOH . R 10 HOH B 10 2010 2010 HOH HOH . R 10 HOH B 11 2011 2011 HOH HOH . R 10 HOH B 12 2012 2012 HOH HOH . R 10 HOH B 13 2013 2013 HOH HOH . R 10 HOH B 14 2014 2014 HOH HOH . R 10 HOH B 15 2015 2015 HOH HOH . R 10 HOH B 16 2016 2016 HOH HOH . R 10 HOH B 17 2017 2017 HOH HOH . R 10 HOH B 18 2018 2018 HOH HOH . R 10 HOH B 19 2019 2019 HOH HOH . R 10 HOH B 20 2020 2020 HOH HOH . R 10 HOH B 21 2021 2021 HOH HOH . R 10 HOH B 22 2022 2022 HOH HOH . R 10 HOH B 23 2023 2023 HOH HOH . R 10 HOH B 24 2024 2024 HOH HOH . R 10 HOH B 25 2025 2025 HOH HOH . R 10 HOH B 26 2026 2026 HOH HOH . R 10 HOH B 27 2027 2027 HOH HOH . R 10 HOH B 28 2028 2028 HOH HOH . R 10 HOH B 29 2029 2029 HOH HOH . R 10 HOH B 30 2030 2030 HOH HOH . S 10 HOH C 1 2001 2001 HOH HOH . S 10 HOH C 2 2002 2002 HOH HOH . S 10 HOH C 3 2003 2003 HOH HOH . S 10 HOH C 4 2004 2004 HOH HOH . S 10 HOH C 5 2005 2005 HOH HOH . S 10 HOH C 6 2006 2006 HOH HOH . S 10 HOH C 7 2007 2007 HOH HOH . S 10 HOH C 8 2008 2008 HOH HOH . S 10 HOH C 9 2009 2009 HOH HOH . S 10 HOH C 10 2010 2010 HOH HOH . S 10 HOH C 11 2011 2011 HOH HOH . S 10 HOH C 12 2012 2012 HOH HOH . S 10 HOH C 13 2013 2013 HOH HOH . S 10 HOH C 14 2014 2014 HOH HOH . S 10 HOH C 15 2015 2015 HOH HOH . S 10 HOH C 16 2016 2016 HOH HOH . S 10 HOH C 17 2017 2017 HOH HOH . S 10 HOH C 18 2018 2018 HOH HOH . S 10 HOH C 19 2019 2019 HOH HOH . S 10 HOH C 20 2020 2020 HOH HOH . T 10 HOH D 1 2001 2001 HOH HOH . T 10 HOH D 2 2002 2002 HOH HOH . T 10 HOH D 3 2003 2003 HOH HOH . T 10 HOH D 4 2004 2004 HOH HOH . T 10 HOH D 5 2005 2005 HOH HOH . T 10 HOH D 6 2006 2006 HOH HOH . T 10 HOH D 7 2007 2007 HOH HOH . T 10 HOH D 8 2008 2008 HOH HOH . T 10 HOH D 9 2009 2009 HOH HOH . T 10 HOH D 10 2010 2010 HOH HOH . T 10 HOH D 11 2011 2011 HOH HOH . T 10 HOH D 12 2012 2012 HOH HOH . T 10 HOH D 13 2013 2013 HOH HOH . T 10 HOH D 14 2014 2014 HOH HOH . T 10 HOH D 15 2015 2015 HOH HOH . T 10 HOH D 16 2016 2016 HOH HOH . T 10 HOH D 17 2017 2017 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 PB ADP . . . F 4 85.228 28.225 47.527 1 46.75 ? PB ADP 302 A 1 HETATM 2 O O1B ADP . . . F 4 85.577 29.076 46.326 1 45.05 ? O1B ADP 302 A 1 HETATM 3 O O2B ADP . . . F 4 83.773 27.899 47.834 1 45.27 ? O2B ADP 302 A 1 HETATM 4 O O3B ADP . . . F 4 86.082 28.514 48.799 1 49.09 ? O3B ADP 302 A 1 HETATM 5 P PA ADP . . . F 4 85.256 25.364 46.646 1 50.74 ? PA ADP 302 A 1 HETATM 6 O O1A ADP . . . F 4 83.941 25.103 47.365 1 50.03 ? O1A ADP 302 A 1 HETATM 7 O O2A ADP . . . F 4 86.316 24.3 46.717 1 54.9 ? O2A ADP 302 A 1 HETATM 8 O O3A ADP . . . F 4 85.849 26.79 47.129 1 51.64 ? O3A ADP 302 A 1 HETATM 9 O O5' ADP . . . F 4 85.479 25.99 45.177 1 53.12 ? O5' ADP 302 A 1 HETATM 10 C C5' ADP . . . F 4 85.059 25.502 43.949 1 55.59 ? C5' ADP 302 A 1 HETATM 11 C C4' ADP . . . F 4 85.972 24.416 43.489 1 58.9 ? C4' ADP 302 A 1 HETATM 12 O O4' ADP . . . F 4 85.226 23.645 42.536 1 64.47 ? O4' ADP 302 A 1 HETATM 13 C C3' ADP . . . F 4 87.187 24.869 42.698 1 62.08 ? C3' ADP 302 A 1 HETATM 14 O O3' ADP . . . F 4 88.29 25.045 43.561 1 64.43 ? O3' ADP 302 A 1 HETATM 15 C C2' ADP . . . F 4 87.459 23.734 41.715 1 61.72 ? C2' ADP 302 A 1 HETATM 16 O O2' ADP . . . F 4 88.589 23.007 42.209 1 60.59 ? O2' ADP 302 A 1 HETATM 17 C C1' ADP . . . F 4 86.16 22.913 41.734 1 60.45 ? C1' ADP 302 A 1 HETATM 18 N N9 ADP . . . F 4 85.514 22.637 40.453 1 59.04 ? N9 ADP 302 A 1 HETATM 19 C C8 ADP . . . F 4 84.792 21.515 40.175 1 63.04 ? C8 ADP 302 A 1 HETATM 20 N N7 ADP . . . F 4 84.306 21.505 38.891 1 61.22 ? N7 ADP 302 A 1 HETATM 21 C C5 ADP . . . F 4 84.714 22.678 38.356 1 60.58 ? C5 ADP 302 A 1 HETATM 22 C C6 ADP . . . F 4 84.582 23.355 37.061 1 60.88 ? C6 ADP 302 A 1 HETATM 23 N N6 ADP . . . F 4 83.92 22.836 36.023 1 63.85 ? N6 ADP 302 A 1 HETATM 24 N N1 ADP . . . F 4 85.159 24.545 36.931 1 63.91 ? N1 ADP 302 A 1 HETATM 25 C C2 ADP . . . F 4 85.836 25.162 37.923 1 61.82 ? C2 ADP 302 A 1 HETATM 26 N N3 ADP . . . F 4 85.991 24.612 39.133 1 59.13 ? N3 ADP 302 A 1 HETATM 27 C C4 ADP . . . F 4 85.483 23.407 39.396 1 58.65 ? C4 ADP 302 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #