data_2VNI # _model_server_result.job_id k30a9CeWyUPbfRO_gN7jIg _model_server_result.datetime_utc '2024-12-10 08:31:56' _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 2vni # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":274}' # _entry.id 2VNI # _exptl.entry_id 2VNI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-2'-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 120 _cell.entry_id 2VNI _cell.length_a 121.116 _cell.length_b 121.116 _cell.length_c 50.574 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VNI _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A2P _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-2'-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 P1 O1P A2P doub 1 n n P1 O2P A2P sing 2 n n P1 O3P A2P sing 3 n n P1 O2' A2P sing 4 n n O2P HOP2 A2P sing 5 n n O3P HOP3 A2P sing 6 n n P2 O4P A2P doub 7 n n P2 O5P A2P sing 8 n n P2 O6P A2P sing 9 n n P2 O5' A2P sing 10 n n O5P HOP5 A2P sing 11 n n O6P HOP6 A2P sing 12 n n O5' C5' A2P sing 13 n n C5' C4' A2P sing 14 n n C5' "H5'1" A2P sing 15 n n C5' "H5'2" A2P sing 16 n n C4' O4' A2P sing 17 n n C4' C3' A2P sing 18 n n C4' H4' A2P sing 19 n n O4' C1' A2P sing 20 n n C3' O3' A2P sing 21 n n C3' C2' A2P sing 22 n n C3' H3' A2P sing 23 n n O3' HO3' A2P sing 24 n n C2' O2' A2P sing 25 n n C2' C1' A2P sing 26 n n C2' H2' A2P sing 27 n n C1' N9 A2P sing 28 n n C1' H1' A2P sing 29 n n N9 C8 A2P sing 30 n y N9 C4 A2P sing 31 n y C8 N7 A2P doub 32 n y C8 H8 A2P sing 33 n n N7 C5 A2P sing 34 n y C5 C6 A2P sing 35 n y C5 C4 A2P doub 36 n y C6 N6 A2P sing 37 n n C6 N1 A2P doub 38 n y N6 HN61 A2P sing 39 n n N6 HN62 A2P sing 40 n n N1 C2 A2P sing 41 n y C2 N3 A2P doub 42 n y C2 H2 A2P sing 43 n n N3 C4 A2P sing 44 n y # _atom_sites.entry_id 2VNI _atom_sites.fract_transf_matrix[1][1] 0.008257 _atom_sites.fract_transf_matrix[1][2] 0.004767 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009534 _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] 0.019773 _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 B 2 FAD A 1 273 273 FAD FAD . C 3 A2P A 1 274 274 A2P A2P . D 4 HTG A 1 275 275 HTG HTG . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 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 P1 A2P . . . C 3 -10.653 60.154 17.032 1 44.12 ? P1 A2P 274 A 1 HETATM 2 O O1P A2P . . . C 3 -10.98 61.466 16.387 1 44.12 ? O1P A2P 274 A 1 HETATM 3 O O2P A2P . . . C 3 -11.86 59.436 17.473 1 44.12 ? O2P A2P 274 A 1 HETATM 4 O O3P A2P . . . C 3 -9.52 60.33 17.98 1 44.12 ? O3P A2P 274 A 1 HETATM 5 P P2 A2P . . . C 3 -14.431 59.891 11.967 1 44.12 ? P2 A2P 274 A 1 HETATM 6 O O4P A2P . . . C 3 -14.787 61.067 12.833 1 44.12 ? O4P A2P 274 A 1 HETATM 7 O O5P A2P . . . C 3 -14.302 60.312 10.523 1 44.12 ? O5P A2P 274 A 1 HETATM 8 O O6P A2P . . . C 3 -15.387 58.778 12.29 1 44.12 ? O6P A2P 274 A 1 HETATM 9 O O5' A2P . . . C 3 -13.005 59.351 12.473 1 44.12 ? O5' A2P 274 A 1 HETATM 10 C C5' A2P . . . C 3 -12.446 58.149 11.974 1 44.12 ? C5' A2P 274 A 1 HETATM 11 C C4' A2P . . . C 3 -11.092 57.931 12.648 1 44.12 ? C4' A2P 274 A 1 HETATM 12 O O4' A2P . . . C 3 -9.991 58.804 12.322 1 44.12 ? O4' A2P 274 A 1 HETATM 13 C C3' A2P . . . C 3 -11.173 57.971 14.175 1 44.12 ? C3' A2P 274 A 1 HETATM 14 O O3' A2P . . . C 3 -10.34 56.98 14.756 1 44.12 ? O3' A2P 274 A 1 HETATM 15 C C2' A2P . . . C 3 -10.679 59.367 14.5 1 44.12 ? C2' A2P 274 A 1 HETATM 16 O O2' A2P . . . C 3 -10.007 59.395 15.755 1 44.12 ? O2' A2P 274 A 1 HETATM 17 C C1' A2P . . . C 3 -9.562 59.527 13.488 1 44.12 ? C1' A2P 274 A 1 HETATM 18 N N9 A2P . . . C 3 -9.238 60.908 13.078 1 44.12 ? N9 A2P 274 A 1 HETATM 19 C C8 A2P . . . C 3 -10.134 61.887 12.757 1 44.12 ? C8 A2P 274 A 1 HETATM 20 N N7 A2P . . . C 3 -9.525 63.031 12.364 1 44.12 ? N7 A2P 274 A 1 HETATM 21 C C5 A2P . . . C 3 -8.219 62.749 12.441 1 44.12 ? C5 A2P 274 A 1 HETATM 22 C C6 A2P . . . C 3 -6.992 63.489 12.15 1 44.12 ? C6 A2P 274 A 1 HETATM 23 N N6 A2P . . . C 3 -7.062 64.772 11.743 1 44.12 ? N6 A2P 274 A 1 HETATM 24 N N1 A2P . . . C 3 -5.829 62.873 12.325 1 44.12 ? N1 A2P 274 A 1 HETATM 25 C C2 A2P . . . C 3 -5.755 61.608 12.763 1 44.12 ? C2 A2P 274 A 1 HETATM 26 N N3 A2P . . . C 3 -6.806 60.839 13.071 1 44.12 ? N3 A2P 274 A 1 HETATM 27 C C4 A2P . . . C 3 -8.014 61.366 12.876 1 44.12 ? C4 A2P 274 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #