data_4V03 # _model_server_result.job_id MpO6YOZL1J7LFHGwGl-hcA _model_server_result.datetime_utc '2024-11-30 23:25:31' _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 4v03 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":303}' # _entry.id 4V03 # _exptl.entry_id 4V03 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _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 71.3 _cell.angle_beta 89.21 _cell.angle_gamma 69.93 _cell.entry_id 4V03 _cell.length_a 36.234 _cell.length_b 51.671 _cell.length_c 69.085 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4V03 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 17 A THR 17 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc2 C O1B ADP . A ADP 303 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc3 D MG MG . A MG 401 1_555 G O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc4 D MG MG . A MG 401 1_555 G O HOH . A HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc5 D MG MG . A MG 401 1_555 G O HOH . A HOH 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc6 D MG MG . A MG 401 1_555 G O HOH . A HOH 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc7 B OG1 THR 17 B THR 17 1_555 F MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc8 E O1B ADP . B ADP 303 1_555 F MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc9 F MG MG . B MG 401 1_555 H O HOH . B HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc10 F MG MG . B MG 401 1_555 H O HOH . B HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc11 F MG MG . B MG 401 1_555 H O HOH . B HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.854 ? metalc ? metalc12 F MG MG . B MG 401 1_555 H O HOH . B HOH 2018 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? # _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 4V03 _atom_sites.fract_transf_matrix[1][1] 0.027598 _atom_sites.fract_transf_matrix[1][2] -0.010083 _atom_sites.fract_transf_matrix[1][3] 0.003197 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020604 _atom_sites.fract_transf_matrix[2][3] -0.007359 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015372 _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 2 ADP A 1 303 303 ADP ADP . D 3 MG A 1 401 401 MG MG . E 2 ADP B 1 303 303 ADP ADP . F 3 MG B 1 401 401 MG MG . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . G 4 HOH A 11 2011 2011 HOH HOH . G 4 HOH A 12 2012 2012 HOH HOH . G 4 HOH A 13 2013 2013 HOH HOH . G 4 HOH A 14 2014 2014 HOH HOH . G 4 HOH A 15 2015 2015 HOH HOH . G 4 HOH A 16 2016 2016 HOH HOH . G 4 HOH A 17 2017 2017 HOH HOH . G 4 HOH A 18 2018 2018 HOH HOH . G 4 HOH A 19 2019 2019 HOH HOH . G 4 HOH A 20 2020 2020 HOH HOH . G 4 HOH A 21 2021 2021 HOH HOH . G 4 HOH A 22 2022 2022 HOH HOH . G 4 HOH A 23 2023 2023 HOH HOH . G 4 HOH A 24 2024 2024 HOH HOH . G 4 HOH A 25 2025 2025 HOH HOH . G 4 HOH A 26 2026 2026 HOH HOH . G 4 HOH A 27 2027 2027 HOH HOH . G 4 HOH A 28 2028 2028 HOH HOH . G 4 HOH A 29 2029 2029 HOH HOH . G 4 HOH A 30 2030 2030 HOH HOH . G 4 HOH A 31 2031 2031 HOH HOH . G 4 HOH A 32 2032 2032 HOH HOH . G 4 HOH A 33 2033 2033 HOH HOH . G 4 HOH A 34 2034 2034 HOH HOH . G 4 HOH A 35 2035 2035 HOH HOH . G 4 HOH A 36 2036 2036 HOH HOH . G 4 HOH A 37 2037 2037 HOH HOH . G 4 HOH A 38 2038 2038 HOH HOH . G 4 HOH A 39 2039 2039 HOH HOH . G 4 HOH A 40 2040 2040 HOH HOH . G 4 HOH A 41 2041 2041 HOH HOH . G 4 HOH A 42 2042 2042 HOH HOH . G 4 HOH A 43 2043 2043 HOH HOH . G 4 HOH A 44 2044 2044 HOH HOH . G 4 HOH A 45 2045 2045 HOH HOH . G 4 HOH A 46 2046 2046 HOH HOH . G 4 HOH A 47 2047 2047 HOH HOH . G 4 HOH A 48 2048 2048 HOH HOH . G 4 HOH A 49 2049 2049 HOH HOH . G 4 HOH A 50 2050 2050 HOH HOH . G 4 HOH A 51 2051 2051 HOH HOH . G 4 HOH A 52 2052 2052 HOH HOH . G 4 HOH A 53 2053 2053 HOH HOH . G 4 HOH A 54 2054 2054 HOH HOH . G 4 HOH A 55 2055 2055 HOH HOH . G 4 HOH A 56 2056 2056 HOH HOH . G 4 HOH A 57 2057 2057 HOH HOH . G 4 HOH A 58 2058 2058 HOH HOH . G 4 HOH A 59 2059 2059 HOH HOH . G 4 HOH A 60 2060 2060 HOH HOH . G 4 HOH A 61 2061 2061 HOH HOH . G 4 HOH A 62 2062 2062 HOH HOH . G 4 HOH A 63 2063 2063 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 HOH HOH . H 4 HOH B 8 2008 2008 HOH HOH . H 4 HOH B 9 2009 2009 HOH HOH . H 4 HOH B 10 2010 2010 HOH HOH . H 4 HOH B 11 2011 2011 HOH HOH . H 4 HOH B 12 2012 2012 HOH HOH . H 4 HOH B 13 2013 2013 HOH HOH . H 4 HOH B 14 2014 2014 HOH HOH . H 4 HOH B 15 2015 2015 HOH HOH . H 4 HOH B 16 2016 2016 HOH HOH . H 4 HOH B 17 2017 2017 HOH HOH . H 4 HOH B 18 2018 2018 HOH HOH . H 4 HOH B 19 2019 2019 HOH HOH . H 4 HOH B 20 2020 2020 HOH HOH . H 4 HOH B 21 2021 2021 HOH HOH . H 4 HOH B 22 2022 2022 HOH HOH . H 4 HOH B 23 2023 2023 HOH HOH . H 4 HOH B 24 2024 2024 HOH HOH . H 4 HOH B 25 2025 2025 HOH HOH . H 4 HOH B 26 2026 2026 HOH HOH . H 4 HOH B 27 2027 2027 HOH HOH . H 4 HOH B 28 2028 2028 HOH HOH . H 4 HOH B 29 2029 2029 HOH HOH . H 4 HOH B 30 2030 2030 HOH HOH . H 4 HOH B 31 2031 2031 HOH HOH . H 4 HOH B 32 2032 2032 HOH HOH . H 4 HOH B 33 2033 2033 HOH HOH . H 4 HOH B 34 2034 2034 HOH HOH . H 4 HOH B 35 2035 2035 HOH HOH . H 4 HOH B 36 2036 2036 HOH HOH . H 4 HOH B 37 2037 2037 HOH HOH . H 4 HOH B 38 2038 2038 HOH HOH . H 4 HOH B 39 2039 2039 HOH HOH . H 4 HOH B 40 2040 2040 HOH HOH . H 4 HOH B 41 2041 2041 HOH HOH . H 4 HOH B 42 2042 2042 HOH HOH . H 4 HOH B 43 2043 2043 HOH HOH . H 4 HOH B 44 2044 2044 HOH HOH . H 4 HOH B 45 2045 2045 HOH HOH . H 4 HOH B 46 2046 2046 HOH HOH . H 4 HOH B 47 2047 2047 HOH HOH . H 4 HOH B 48 2048 2048 HOH HOH . H 4 HOH B 49 2049 2049 HOH HOH . H 4 HOH B 50 2050 2050 HOH HOH . H 4 HOH B 51 2051 2051 HOH HOH . H 4 HOH B 52 2052 2052 HOH HOH . H 4 HOH B 53 2053 2053 HOH HOH . H 4 HOH B 54 2054 2054 HOH HOH . H 4 HOH B 55 2055 2055 HOH HOH . H 4 HOH B 56 2056 2056 HOH HOH . H 4 HOH B 57 2057 2057 HOH HOH . H 4 HOH B 58 2058 2058 HOH HOH . H 4 HOH B 59 2059 2059 HOH HOH . H 4 HOH B 60 2060 2060 HOH HOH . H 4 HOH B 61 2061 2061 HOH HOH . H 4 HOH B 62 2062 2062 HOH HOH . H 4 HOH B 63 2063 2063 HOH HOH . H 4 HOH B 64 2064 2064 HOH HOH . H 4 HOH B 65 2065 2065 HOH HOH . H 4 HOH B 66 2066 2066 HOH HOH . H 4 HOH B 67 2067 2067 HOH HOH . H 4 HOH B 68 2068 2068 HOH HOH . H 4 HOH B 69 2069 2069 HOH HOH . H 4 HOH B 70 2070 2070 HOH HOH . H 4 HOH B 71 2071 2071 HOH HOH . H 4 HOH B 72 2072 2072 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 . . . C 2 3.409 0.159 34.84 1 14.14 ? PB ADP 303 A 1 HETATM 2 O O1B ADP . . . C 2 3.09 -0.714 33.63 1 14.74 ? O1B ADP 303 A 1 HETATM 3 O O2B ADP . . . C 2 4.903 0.403 34.972 1 18.91 ? O2B ADP 303 A 1 HETATM 4 O O3B ADP . . . C 2 2.706 -0.15 36.112 1 18.03 ? O3B ADP 303 A 1 HETATM 5 P PA ADP . . . C 2 1.636 1.859 33.301 1 16.03 ? PA ADP 303 A 1 HETATM 6 O O1A ADP . . . C 2 2.277 1.77 31.929 1 14.16 ? O1A ADP 303 A 1 HETATM 7 O O2A ADP . . . C 2 0.408 1.079 33.611 1 14.63 ? O2A ADP 303 A 1 HETATM 8 O O3A ADP . . . C 2 2.795 1.587 34.406 1 12.62 ? O3A ADP 303 A 1 HETATM 9 O O5' ADP . . . C 2 1.267 3.415 33.557 1 22.61 ? O5' ADP 303 A 1 HETATM 10 C C5' ADP . . . C 2 0.965 3.988 34.832 1 21.65 ? C5' ADP 303 A 1 HETATM 11 C C4' ADP . . . C 2 0.048 5.18 34.607 1 18.2 ? C4' ADP 303 A 1 HETATM 12 O O4' ADP . . . C 2 0.789 6.339 34.195 1 25.28 ? O4' ADP 303 A 1 HETATM 13 C C3' ADP . . . C 2 -0.927 4.86 33.486 1 28.36 ? C3' ADP 303 A 1 HETATM 14 O O3' ADP . . . C 2 -2.217 5.356 33.848 1 33.66 ? O3' ADP 303 A 1 HETATM 15 C C2' ADP . . . C 2 -0.366 5.577 32.27 1 22.96 ? C2' ADP 303 A 1 HETATM 16 O O2' ADP . . . C 2 -1.325 6.033 31.306 1 25.22 ? O2' ADP 303 A 1 HETATM 17 C C1' ADP . . . C 2 0.321 6.766 32.907 1 18.74 ? C1' ADP 303 A 1 HETATM 18 N N9 ADP . . . C 2 1.481 7.215 32.13 1 20.47 ? N9 ADP 303 A 1 HETATM 19 C C8 ADP . . . C 2 2.467 6.454 31.637 1 18.04 ? C8 ADP 303 A 1 HETATM 20 N N7 ADP . . . C 2 3.377 7.239 31.012 1 18.75 ? N7 ADP 303 A 1 HETATM 21 C C5 ADP . . . C 2 2.954 8.517 31.106 1 15.11 ? C5 ADP 303 A 1 HETATM 22 C C6 ADP . . . C 2 3.441 9.849 30.675 1 17.55 ? C6 ADP 303 A 1 HETATM 23 N N6 ADP . . . C 2 4.58 9.98 29.972 1 14.1 ? N6 ADP 303 A 1 HETATM 24 N N1 ADP . . . C 2 2.695 10.921 30.982 1 17.8 ? N1 ADP 303 A 1 HETATM 25 C C2 ADP . . . C 2 1.546 10.809 31.662 1 13.55 ? C2 ADP 303 A 1 HETATM 26 N N3 ADP . . . C 2 1.065 9.644 32.081 1 16.67 ? N3 ADP 303 A 1 HETATM 27 C C4 ADP . . . C 2 1.714 8.49 31.841 1 16.75 ? C4 ADP 303 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #