data_2VF8 # _model_server_result.job_id aUh5l4qnKdAYNNsWMmdBtw _model_server_result.datetime_utc '2024-12-21 12:56:13' _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 2vf8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1844}' # _entry.id 2VF8 # _exptl.entry_id 2VF8 _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 4 _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 2VF8 _cell.length_a 149.632 _cell.length_b 171.04 _cell.length_c 204.205 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VF8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PQS monomeric 1 software_defined_assembly 2 PQS monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 1 1 A,C,D,E,F,G,H,I,T 2 1 B,J,K,L,M,N,O,P,Q,R,S,U 3 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 D N N ? 2 J N N ? 2 K 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 SG CYS 151 A CYS 151 1_555 E ZN ZN . A ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc2 A SG CYS 154 A CYS 154 1_555 E ZN ZN . A ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc3 A SG CYS 287 A CYS 287 1_555 E ZN ZN . A ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc4 A SG CYS 290 A CYS 290 1_555 E ZN ZN . A ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc5 A SG CYS 641 A CYS 641 1_555 F ZN ZN . A ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc6 B SG CYS 151 B CYS 151 1_555 L ZN ZN . B ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc7 B SG CYS 154 B CYS 154 1_555 L ZN ZN . B ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc8 B SG CYS 287 B CYS 287 1_555 L ZN ZN . B ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc9 B SG CYS 290 B CYS 290 1_555 L ZN ZN . B ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc10 B SG CYS 641 B CYS 641 1_555 M ZN ZN . B ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc11 B SG CYS 644 B CYS 644 1_555 M ZN ZN . B ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc12 B SG CYS 664 B CYS 664 1_555 M ZN ZN . B ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc13 B SG CYS 667 B CYS 667 1_555 M ZN ZN . B ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? # _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 2VF8 _atom_sites.fract_transf_matrix[1][1] 0.006683 _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] 0.005847 _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] 0.004897 _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 1843 1843 ADP ADP . D 2 ADP A 1 1844 1844 ADP ADP . E 3 ZN A 1 1845 1845 ZN ZN . F 3 ZN A 1 1846 1846 ZN ZN . G 4 SO4 A 1 1847 1847 SO4 SO4 . H 4 SO4 A 1 1848 1848 SO4 SO4 . I 4 SO4 A 1 1849 1849 SO4 SO4 . J 2 ADP B 1 1843 1843 ADP ADP . K 2 ADP B 1 1844 1844 ADP ADP . L 3 ZN B 1 1845 1845 ZN ZN . M 3 ZN B 1 1846 1846 ZN ZN . N 4 SO4 B 1 1847 1847 SO4 SO4 . O 4 SO4 B 1 1848 1848 SO4 SO4 . P 4 SO4 B 1 1849 1849 SO4 SO4 . Q 4 SO4 B 1 1850 1850 SO4 SO4 . R 4 SO4 B 1 1851 1851 SO4 SO4 . S 5 PO4 B 1 1852 1852 PO4 PO4 . T 6 HOH A 1 2001 2001 HOH HOH . T 6 HOH A 2 2002 2002 HOH HOH . T 6 HOH A 3 2003 2003 HOH HOH . T 6 HOH A 4 2004 2004 HOH HOH . T 6 HOH A 5 2005 2005 HOH HOH . T 6 HOH A 6 2006 2006 HOH HOH . T 6 HOH A 7 2007 2007 HOH HOH . T 6 HOH A 8 2008 2008 HOH HOH . T 6 HOH A 9 2009 2009 HOH HOH . T 6 HOH A 10 2010 2010 HOH HOH . T 6 HOH A 11 2011 2011 HOH HOH . T 6 HOH A 12 2012 2012 HOH HOH . T 6 HOH A 13 2013 2013 HOH HOH . T 6 HOH A 14 2014 2014 HOH HOH . T 6 HOH A 15 2015 2015 HOH HOH . T 6 HOH A 16 2016 2016 HOH HOH . T 6 HOH A 17 2017 2017 HOH HOH . T 6 HOH A 18 2018 2018 HOH HOH . T 6 HOH A 19 2019 2019 HOH HOH . T 6 HOH A 20 2020 2020 HOH HOH . T 6 HOH A 21 2021 2021 HOH HOH . T 6 HOH A 22 2022 2022 HOH HOH . T 6 HOH A 23 2023 2023 HOH HOH . T 6 HOH A 24 2024 2024 HOH HOH . T 6 HOH A 25 2025 2025 HOH HOH . T 6 HOH A 26 2026 2026 HOH HOH . T 6 HOH A 27 2027 2027 HOH HOH . T 6 HOH A 28 2028 2028 HOH HOH . T 6 HOH A 29 2029 2029 HOH HOH . T 6 HOH A 30 2030 2030 HOH HOH . T 6 HOH A 31 2031 2031 HOH HOH . T 6 HOH A 32 2032 2032 HOH HOH . T 6 HOH A 33 2033 2033 HOH HOH . T 6 HOH A 34 2034 2034 HOH HOH . T 6 HOH A 35 2035 2035 HOH HOH . T 6 HOH A 36 2036 2036 HOH HOH . T 6 HOH A 37 2037 2037 HOH HOH . U 6 HOH B 1 2001 2001 HOH HOH . U 6 HOH B 2 2002 2002 HOH HOH . U 6 HOH B 3 2003 2003 HOH HOH . U 6 HOH B 4 2004 2004 HOH HOH . U 6 HOH B 5 2005 2005 HOH HOH . U 6 HOH B 6 2006 2006 HOH HOH . U 6 HOH B 7 2007 2007 HOH HOH . U 6 HOH B 8 2008 2008 HOH HOH . U 6 HOH B 9 2009 2009 HOH HOH . U 6 HOH B 10 2010 2010 HOH HOH . U 6 HOH B 11 2011 2011 HOH HOH . U 6 HOH B 12 2012 2012 HOH HOH . U 6 HOH B 13 2013 2013 HOH HOH . U 6 HOH B 14 2014 2014 HOH HOH . U 6 HOH B 15 2015 2015 HOH HOH . U 6 HOH B 16 2016 2016 HOH HOH . U 6 HOH B 17 2017 2017 HOH HOH . U 6 HOH B 18 2018 2018 HOH HOH . U 6 HOH B 19 2019 2019 HOH HOH . U 6 HOH B 20 2020 2020 HOH HOH . U 6 HOH B 21 2021 2021 HOH HOH . U 6 HOH B 22 2022 2022 HOH HOH . U 6 HOH B 23 2023 2023 HOH HOH . U 6 HOH B 24 2024 2024 HOH HOH . U 6 HOH B 25 2025 2025 HOH HOH . U 6 HOH B 26 2026 2026 HOH HOH . U 6 HOH B 27 2027 2027 HOH HOH . U 6 HOH B 28 2028 2028 HOH HOH . U 6 HOH B 29 2029 2029 HOH HOH . U 6 HOH B 30 2030 2030 HOH HOH . U 6 HOH B 31 2031 2031 HOH HOH . U 6 HOH B 32 2032 2032 HOH HOH . U 6 HOH B 33 2033 2033 HOH HOH . U 6 HOH B 34 2034 2034 HOH HOH . U 6 HOH B 35 2035 2035 HOH HOH . U 6 HOH B 36 2036 2036 HOH HOH . U 6 HOH B 37 2037 2037 HOH HOH . U 6 HOH B 38 2038 2038 HOH HOH . U 6 HOH B 39 2039 2039 HOH HOH . U 6 HOH B 40 2040 2040 HOH HOH . U 6 HOH B 41 2041 2041 HOH HOH . U 6 HOH B 42 2042 2042 HOH HOH . U 6 HOH B 43 2043 2043 HOH HOH . U 6 HOH B 44 2044 2044 HOH HOH . U 6 HOH B 45 2045 2045 HOH HOH . U 6 HOH B 46 2046 2046 HOH HOH . U 6 HOH B 47 2047 2047 HOH HOH . U 6 HOH B 48 2048 2048 HOH HOH . U 6 HOH B 49 2049 2049 HOH HOH . U 6 HOH B 50 2050 2050 HOH HOH . U 6 HOH B 51 2051 2051 HOH HOH . U 6 HOH B 52 2052 2052 HOH HOH . U 6 HOH B 53 2053 2053 HOH HOH . U 6 HOH B 54 2054 2054 HOH HOH . U 6 HOH B 55 2055 2055 HOH HOH . U 6 HOH B 56 2056 2056 HOH HOH . U 6 HOH B 57 2057 2057 HOH HOH . U 6 HOH B 58 2058 2058 HOH HOH . U 6 HOH B 59 2059 2059 HOH HOH . U 6 HOH B 60 2060 2060 HOH HOH . U 6 HOH B 61 2061 2061 HOH HOH . U 6 HOH B 62 2062 2062 HOH HOH . U 6 HOH B 63 2063 2063 HOH HOH . U 6 HOH B 64 2064 2064 HOH HOH . U 6 HOH B 65 2065 2065 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 . . . D 2 74.033 125.884 110.078 1 32.2 ? PB ADP 1844 A 1 HETATM 2 O O1B ADP . . . D 2 73.405 126.265 108.744 1 31.3 ? O1B ADP 1844 A 1 HETATM 3 O O2B ADP . . . D 2 72.96 125.823 111.1 1 33.22 ? O2B ADP 1844 A 1 HETATM 4 O O3B ADP . . . D 2 75.328 126.49 110.521 1 32.18 ? O3B ADP 1844 A 1 HETATM 5 P PA ADP . . . D 2 73.69 123.027 109.937 1 31.77 ? PA ADP 1844 A 1 HETATM 6 O O1A ADP . . . D 2 72.354 123.284 109.301 1 34.9 ? O1A ADP 1844 A 1 HETATM 7 O O2A ADP . . . D 2 73.669 122.668 111.402 1 33.75 ? O2A ADP 1844 A 1 HETATM 8 O O3A ADP . . . D 2 74.592 124.361 109.895 1 34.86 ? O3A ADP 1844 A 1 HETATM 9 O O5' ADP . . . D 2 74.521 122.109 108.895 1 32.15 ? O5' ADP 1844 A 1 HETATM 10 C C5' ADP . . . D 2 75.613 121.347 109.356 1 41.13 ? C5' ADP 1844 A 1 HETATM 11 C C4' ADP . . . D 2 75.766 120.038 108.585 1 44.76 ? C4' ADP 1844 A 1 HETATM 12 O O4' ADP . . . D 2 74.63 119.252 108.843 1 45.71 ? O4' ADP 1844 A 1 HETATM 13 C C3' ADP . . . D 2 75.824 120.257 107.096 1 47.24 ? C3' ADP 1844 A 1 HETATM 14 O O3' ADP . . . D 2 76.81 119.334 106.688 1 50.2 ? O3' ADP 1844 A 1 HETATM 15 C C2' ADP . . . D 2 74.514 119.794 106.526 1 47.21 ? C2' ADP 1844 A 1 HETATM 16 O O2' ADP . . . D 2 74.743 119.027 105.331 1 47.34 ? O2' ADP 1844 A 1 HETATM 17 C C1' ADP . . . D 2 74.002 118.916 107.624 1 48.45 ? C1' ADP 1844 A 1 HETATM 18 N N9 ADP . . . D 2 72.587 119.092 107.914 1 49.15 ? N9 ADP 1844 A 1 HETATM 19 C C8 ADP . . . D 2 72 120.161 108.46 1 50.59 ? C8 ADP 1844 A 1 HETATM 20 N N7 ADP . . . D 2 70.672 119.918 108.617 1 50.98 ? N7 ADP 1844 A 1 HETATM 21 C C5 ADP . . . D 2 70.436 118.648 108.157 1 51.25 ? C5 ADP 1844 A 1 HETATM 22 C C6 ADP . . . D 2 69.277 117.717 108.005 1 51.38 ? C6 ADP 1844 A 1 HETATM 23 N N6 ADP . . . D 2 68.019 118.108 108.4 1 51.73 ? N6 ADP 1844 A 1 HETATM 24 N N1 ADP . . . D 2 69.496 116.476 107.487 1 49.88 ? N1 ADP 1844 A 1 HETATM 25 C C2 ADP . . . D 2 70.713 116.076 107.093 1 49.8 ? C2 ADP 1844 A 1 HETATM 26 N N3 ADP . . . D 2 71.788 116.856 107.207 1 49.88 ? N3 ADP 1844 A 1 HETATM 27 C C4 ADP . . . D 2 71.717 118.108 107.723 1 49.8 ? C4 ADP 1844 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 91 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #