data_2VX9 # _model_server_result.job_id 0vOXH1-S5un8-yYygoXPBQ _model_server_result.datetime_utc '2024-11-08 04:00:07' _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 2vx9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1066}' # _entry.id 2VX9 # _exptl.entry_id 2VX9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 2VX9 _cell.length_a 142.94 _cell.length_b 142.94 _cell.length_c 142.94 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VX9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 210 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'F 41 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10,11,12 # 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' 34_555 -y+1/2,z,-x+1/2 0 -1 0 0 0 1 -1 0 0 71.47 0 71.47 3 'crystal symmetry operation' 55_555 -z+1/2,-x+1/2,y 0 0 -1 -1 0 0 0 1 0 71.47 71.47 0 4 'crystal symmetry operation' 11_465 y-1/2,-z+1,-x+1/2 0 1 0 0 0 -1 -1 0 0 -71.47 142.94 71.47 5 'crystal symmetry operation' 8_556 -z+1/2,x+1/2,-y+1 0 0 -1 1 0 0 0 -1 0 71.47 71.47 142.94 6 'crystal symmetry operation' 77_455 z-1/2,x+1/2,y 0 0 1 1 0 0 0 1 0 -71.47 71.47 0 7 'crystal symmetry operation' 52_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 142.94 142.94 8 'crystal symmetry operation' 26_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 142.94 0 9 'crystal symmetry operation' 84_565 -y+1/2,-z+1,x+1/2 0 -1 0 0 0 -1 1 0 0 71.47 142.94 71.47 10 'crystal symmetry operation' 30_456 z-1/2,-x+1/2,-y+1 0 0 1 -1 0 0 0 -1 0 -71.47 71.47 142.94 11 'crystal symmetry operation' 57_455 y-1/2,z,x+1/2 0 1 0 0 0 1 1 0 0 -71.47 0 71.47 12 'crystal symmetry operation' 75_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 142.94 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N ? 3 I 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 OE2 GLU 14 A GLU 14 1_555 C NA NA . A NA 1065 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc2 A OD2 ASP 41 A ASP 41 8_556 I NA NA . A NA 1071 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc3 B O2' RBF . A RBF 1064 1_555 D NA NA . A NA 1066 55_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.997 ? metalc ? metalc4 B O3' RBF . A RBF 1064 1_555 D NA NA . A NA 1066 55_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc5 B O2' RBF . A RBF 1064 34_555 D NA NA . A NA 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.997 ? metalc ? metalc6 B O3' RBF . A RBF 1064 34_555 D NA NA . A NA 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc7 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc8 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2025 43_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc9 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2027 43_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc10 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2033 43_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc11 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2056 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc12 E NA NA . A NA 1067 1_555 F CL CL . A CL 1068 11_465 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc13 E NA NA . A NA 1067 1_555 F CL CL . A CL 1068 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc14 E NA NA . A NA 1067 1_555 F CL CL . A CL 1068 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc15 E NA NA . A NA 1067 1_555 G CL CL . A CL 1069 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc16 E NA NA . A NA 1067 1_555 G CL CL . A CL 1069 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc17 E NA NA . A NA 1067 1_555 G CL CL . A CL 1069 11_465 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc18 E NA NA . A NA 1067 1_555 J O HOH . A HOH 2065 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc19 E NA NA . A NA 1067 1_555 J O HOH . A HOH 2065 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc20 E NA NA . A NA 1067 1_555 J O HOH . A HOH 2065 11_465 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc21 I NA NA . A NA 1071 1_555 J O HOH . A HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2VX9 _atom_sites.fract_transf_matrix[1][1] 0.006996 _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] 0.006996 _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] 0.006996 _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 RBF A 1 1064 1064 RBF RBF . C 3 NA A 1 1065 1065 NA NA . D 3 NA A 1 1066 1066 NA NA . E 3 NA A 1 1067 1067 NA NA . F 4 CL A 1 1068 1068 CL CL . G 4 CL A 1 1069 1069 CL CL . H 4 CL A 1 1070 1070 CL CL . I 3 NA A 1 1071 1071 NA NA . J 5 HOH A 1 2001 2001 HOH HOH . J 5 HOH A 2 2002 2002 HOH HOH . J 5 HOH A 3 2003 2003 HOH HOH . J 5 HOH A 4 2004 2004 HOH HOH . J 5 HOH A 5 2005 2005 HOH HOH . J 5 HOH A 6 2006 2006 HOH HOH . J 5 HOH A 7 2007 2007 HOH HOH . J 5 HOH A 8 2008 2008 HOH HOH . J 5 HOH A 9 2009 2009 HOH HOH . J 5 HOH A 10 2010 2010 HOH HOH . J 5 HOH A 11 2011 2011 HOH HOH . J 5 HOH A 12 2012 2012 HOH HOH . J 5 HOH A 13 2013 2013 HOH HOH . J 5 HOH A 14 2014 2014 HOH HOH . J 5 HOH A 15 2015 2015 HOH HOH . J 5 HOH A 16 2016 2016 HOH HOH . J 5 HOH A 17 2017 2017 HOH HOH . J 5 HOH A 18 2018 2018 HOH HOH . J 5 HOH A 19 2019 2019 HOH HOH . J 5 HOH A 20 2020 2020 HOH HOH . J 5 HOH A 21 2021 2021 HOH HOH . J 5 HOH A 22 2022 2022 HOH HOH . J 5 HOH A 23 2023 2023 HOH HOH . J 5 HOH A 24 2024 2024 HOH HOH . J 5 HOH A 25 2025 2025 HOH HOH . J 5 HOH A 26 2026 2026 HOH HOH . J 5 HOH A 27 2027 2027 HOH HOH . J 5 HOH A 28 2028 2028 HOH HOH . J 5 HOH A 29 2029 2029 HOH HOH . J 5 HOH A 30 2030 2030 HOH HOH . J 5 HOH A 31 2031 2031 HOH HOH . J 5 HOH A 32 2032 2032 HOH HOH . J 5 HOH A 33 2033 2033 HOH HOH . J 5 HOH A 34 2034 2034 HOH HOH . J 5 HOH A 35 2035 2035 HOH HOH . J 5 HOH A 36 2036 2036 HOH HOH . J 5 HOH A 37 2037 2037 HOH HOH . J 5 HOH A 38 2038 2038 HOH HOH . J 5 HOH A 39 2039 2039 HOH HOH . J 5 HOH A 40 2040 2040 HOH HOH . J 5 HOH A 41 2041 2041 HOH HOH . J 5 HOH A 42 2042 2042 HOH HOH . J 5 HOH A 43 2043 2043 HOH HOH . J 5 HOH A 44 2044 2044 HOH HOH . J 5 HOH A 45 2045 2045 HOH HOH . J 5 HOH A 46 2046 2046 HOH HOH . J 5 HOH A 47 2047 2047 HOH HOH . J 5 HOH A 48 2048 2048 HOH HOH . J 5 HOH A 49 2049 2049 HOH HOH . J 5 HOH A 50 2050 2050 HOH HOH . J 5 HOH A 51 2051 2051 HOH HOH . J 5 HOH A 52 2052 2052 HOH HOH . J 5 HOH A 53 2053 2053 HOH HOH . J 5 HOH A 54 2054 2054 HOH HOH . J 5 HOH A 55 2055 2055 HOH HOH . J 5 HOH A 56 2056 2056 HOH HOH . J 5 HOH A 57 2057 2057 HOH HOH . J 5 HOH A 58 2058 2058 HOH HOH . J 5 HOH A 59 2059 2059 HOH HOH . J 5 HOH A 60 2060 2060 HOH HOH . J 5 HOH A 61 2061 2061 HOH HOH . J 5 HOH A 62 2062 2062 HOH HOH . J 5 HOH A 63 2063 2063 HOH HOH . J 5 HOH A 64 2064 2064 HOH HOH . J 5 HOH A 65 2065 2065 HOH HOH . J 5 HOH A 66 2066 2066 HOH HOH . J 5 HOH A 67 2067 2067 HOH HOH . J 5 HOH A 68 2068 2068 HOH HOH . J 5 HOH A 69 2069 2069 HOH HOH . J 5 HOH A 70 2070 2070 HOH HOH . J 5 HOH A 71 2071 2071 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x 1.363 _atom_site.Cartn_y 66.964 _atom_site.Cartn_z 45.724 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 27.54 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1066 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #