data_2VED # _model_server_result.job_id -N_srxV404jdBIxlw71mcw _model_server_result.datetime_utc '2024-11-29 06:42:43' _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 2ved # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2227}' # _entry.id 2VED # _exptl.entry_id 2VED _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2VED _cell.length_a 163.2 _cell.length_b 163.2 _cell.length_c 57.2 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VED _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details 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 1,2,3,4 # 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' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 3 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 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 OG SER 97 A SER 1056 1_555 D MG MG . A MG 2228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 C O2B ADP . A ADP 2227 1_555 D MG MG . A MG 2228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc3 B OG SER 97 B SER 1056 1_555 F MG MG . B MG 2230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc4 E O2B ADP . B ADP 2229 1_555 F MG MG . B MG 2230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? # _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 2VED _atom_sites.fract_transf_matrix[1][1] 0.006127 _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] 0.006127 _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] 0.017483 _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 2227 2227 ADP ADP . D 3 MG A 1 2228 2228 MG MG . E 2 ADP B 1 2229 2229 ADP ADP . F 3 MG B 1 2230 2230 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 . 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 . # 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 46.203 19.347 2.619 1 18.53 ? PB ADP 2227 A 1 HETATM 2 O O1B ADP . . . C 2 47.202 18.39 1.996 1 15.1 ? O1B ADP 2227 A 1 HETATM 3 O O2B ADP . . . C 2 46.473 19.686 4.067 1 15.69 ? O2B ADP 2227 A 1 HETATM 4 O O3B ADP . . . C 2 44.766 18.964 2.3 1 18.25 ? O3B ADP 2227 A 1 HETATM 5 P PA ADP . . . C 2 47.066 22.061 2.399 1 16.78 ? PA ADP 2227 A 1 HETATM 6 O O1A ADP . . . C 2 48.512 21.835 2.831 1 15.54 ? O1A ADP 2227 A 1 HETATM 7 O O2A ADP . . . C 2 46.069 22.595 3.403 1 15.85 ? O2A ADP 2227 A 1 HETATM 8 O O3A ADP . . . C 2 46.45 20.7 1.778 1 18.24 ? O3A ADP 2227 A 1 HETATM 9 O O5' ADP . . . C 2 46.99 22.931 1.049 1 13.95 ? O5' ADP 2227 A 1 HETATM 10 C C5' ADP . . . C 2 47.732 22.567 -0.092 1 14.24 ? C5' ADP 2227 A 1 HETATM 11 C C4' ADP . . . C 2 47.983 23.862 -0.882 1 16.6 ? C4' ADP 2227 A 1 HETATM 12 O O4' ADP . . . C 2 46.763 24.344 -1.483 1 20.04 ? O4' ADP 2227 A 1 HETATM 13 C C3' ADP . . . C 2 48.448 25.049 -0.068 1 17.18 ? C3' ADP 2227 A 1 HETATM 14 O O3' ADP . . . C 2 49.401 25.759 -0.872 1 13.67 ? O3' ADP 2227 A 1 HETATM 15 C C2' ADP . . . C 2 47.175 25.88 0.147 1 18.29 ? C2' ADP 2227 A 1 HETATM 16 O O2' ADP . . . C 2 47.315 27.278 0.446 1 20.6 ? O2' ADP 2227 A 1 HETATM 17 C C1' ADP . . . C 2 46.465 25.701 -1.159 1 18.22 ? C1' ADP 2227 A 1 HETATM 18 N N9 ADP . . . C 2 45.024 25.975 -0.96 1 19.44 ? N9 ADP 2227 A 1 HETATM 19 C C8 ADP . . . C 2 44.228 25.621 0.08 1 19.47 ? C8 ADP 2227 A 1 HETATM 20 N N7 ADP . . . C 2 42.962 26.08 -0.103 1 19.15 ? N7 ADP 2227 A 1 HETATM 21 C C5 ADP . . . C 2 42.946 26.751 -1.272 1 17.6 ? C5 ADP 2227 A 1 HETATM 22 C C6 ADP . . . C 2 41.97 27.519 -2.064 1 17.45 ? C6 ADP 2227 A 1 HETATM 23 N N6 ADP . . . C 2 40.695 27.663 -1.681 1 19.33 ? N6 ADP 2227 A 1 HETATM 24 N N1 ADP . . . C 2 42.353 28.061 -3.227 1 18.9 ? N1 ADP 2227 A 1 HETATM 25 C C2 ADP . . . C 2 43.616 27.924 -3.668 1 19.5 ? C2 ADP 2227 A 1 HETATM 26 N N3 ADP . . . C 2 44.576 27.266 -2.999 1 19.5 ? N3 ADP 2227 A 1 HETATM 27 C C4 ADP . . . C 2 44.299 26.672 -1.821 1 18.74 ? C4 ADP 2227 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #