data_2YPD # _model_server_result.job_id 3wCbQ30Dlol-H0qz4hsHug _model_server_result.datetime_utc '2024-11-02 05:25:32' _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 2ypd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":3504}' # _entry.id 2YPD # _exptl.entry_id 2YPD _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 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 2YPD _cell.length_a 45.718 _cell.length_b 112.206 _cell.length_c 165.173 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 2 21 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,P 1 1 B,J,K,L,M,N,O,Q 2 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 ? 3 I N N ? 3 O 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 P O HOH . A HOH 2071 1_555 G HG EMT . A EMT 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc2 A O CYS 8 A CYS 2163 1_555 C HG EMT . A EMT 3498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.127 ? metalc ? metalc3 A SG CYS 8 A CYS 2163 1_555 C HG EMT . A EMT 3498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc4 A SG CYS 30 A CYS 2185 1_555 E HG EMT . A EMT 3500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? metalc ? metalc5 A SG CYS 70 A CYS 2225 1_555 F HG EMT . A EMT 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc6 A OD1 ASP 108 A ASP 2263 1_555 G HG EMT . A EMT 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? metalc ? metalc7 A O THR 177 A THR 2332 1_555 F HG EMT . A EMT 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.193 ? metalc ? metalc8 A SG CYS 293 A CYS 2448 1_555 C HG EMT . A EMT 3498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.285 ? metalc ? metalc9 B SG CYS 8 B CYS 2163 1_555 K HG EMT . B EMT 3499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc10 B O CYS 8 B CYS 2163 1_555 K HG EMT . B EMT 3499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.097 ? metalc ? metalc11 B SG CYS 30 B CYS 2185 1_555 L HG EMT . B EMT 3500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc12 B OD1 ASP 108 B ASP 2263 1_555 M HG EMT . B EMT 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? metalc ? metalc13 B SG CYS 293 B CYS 2448 1_555 K HG EMT . B EMT 3499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? # _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 2YPD _atom_sites.fract_transf_matrix[1][1] 0.021873 _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] 0.008912 _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] 0.006054 _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 EMT A 1 3498 3498 EMT EMT . D 2 EMT A 1 3499 3499 EMT EMT . E 2 EMT A 1 3500 3500 EMT EMT . F 2 EMT A 1 3501 3501 EMT EMT . G 2 EMT A 1 3502 3502 EMT EMT . H 2 EMT A 1 3503 3503 EMT EMT . I 3 NA A 1 3504 3504 NA NA . J 2 EMT B 1 3498 3498 EMT EMT . K 2 EMT B 1 3499 3499 EMT EMT . L 2 EMT B 1 3500 3500 EMT EMT . M 2 EMT B 1 3501 3501 EMT EMT . N 2 EMT B 1 3502 3502 EMT EMT . O 3 NA B 1 3503 3503 NA NA . P 4 HOH A 1 2001 2001 HOH HOH . P 4 HOH A 2 2002 2002 HOH HOH . P 4 HOH A 3 2003 2003 HOH HOH . P 4 HOH A 4 2004 2004 HOH HOH . P 4 HOH A 5 2005 2005 HOH HOH . P 4 HOH A 6 2006 2006 HOH HOH . P 4 HOH A 7 2007 2007 HOH HOH . P 4 HOH A 8 2008 2008 HOH HOH . P 4 HOH A 9 2009 2009 HOH HOH . P 4 HOH A 10 2010 2010 HOH HOH . P 4 HOH A 11 2011 2011 HOH HOH . P 4 HOH A 12 2012 2012 HOH HOH . P 4 HOH A 13 2013 2013 HOH HOH . P 4 HOH A 14 2014 2014 HOH HOH . P 4 HOH A 15 2015 2015 HOH HOH . P 4 HOH A 16 2016 2016 HOH HOH . P 4 HOH A 17 2017 2017 HOH HOH . P 4 HOH A 18 2018 2018 HOH HOH . P 4 HOH A 19 2019 2019 HOH HOH . P 4 HOH A 20 2020 2020 HOH HOH . P 4 HOH A 21 2021 2021 HOH HOH . P 4 HOH A 22 2022 2022 HOH HOH . P 4 HOH A 23 2023 2023 HOH HOH . P 4 HOH A 24 2024 2024 HOH HOH . P 4 HOH A 25 2025 2025 HOH HOH . P 4 HOH A 26 2026 2026 HOH HOH . P 4 HOH A 27 2027 2027 HOH HOH . P 4 HOH A 28 2028 2028 HOH HOH . P 4 HOH A 29 2029 2029 HOH HOH . P 4 HOH A 30 2030 2030 HOH HOH . P 4 HOH A 31 2031 2031 HOH HOH . P 4 HOH A 32 2032 2032 HOH HOH . P 4 HOH A 33 2033 2033 HOH HOH . P 4 HOH A 34 2034 2034 HOH HOH . P 4 HOH A 35 2035 2035 HOH HOH . P 4 HOH A 36 2036 2036 HOH HOH . P 4 HOH A 37 2037 2037 HOH HOH . P 4 HOH A 38 2038 2038 HOH HOH . P 4 HOH A 39 2039 2039 HOH HOH . P 4 HOH A 40 2040 2040 HOH HOH . P 4 HOH A 41 2041 2041 HOH HOH . P 4 HOH A 42 2042 2042 HOH HOH . P 4 HOH A 43 2043 2043 HOH HOH . P 4 HOH A 44 2044 2044 HOH HOH . P 4 HOH A 45 2045 2045 HOH HOH . P 4 HOH A 46 2046 2046 HOH HOH . P 4 HOH A 47 2047 2047 HOH HOH . P 4 HOH A 48 2048 2048 HOH HOH . P 4 HOH A 49 2049 2049 HOH HOH . P 4 HOH A 50 2050 2050 HOH HOH . P 4 HOH A 51 2051 2051 HOH HOH . P 4 HOH A 52 2052 2052 HOH HOH . P 4 HOH A 53 2053 2053 HOH HOH . P 4 HOH A 54 2054 2054 HOH HOH . P 4 HOH A 55 2055 2055 HOH HOH . P 4 HOH A 56 2056 2056 HOH HOH . P 4 HOH A 57 2057 2057 HOH HOH . P 4 HOH A 58 2058 2058 HOH HOH . P 4 HOH A 59 2059 2059 HOH HOH . P 4 HOH A 60 2060 2060 HOH HOH . P 4 HOH A 61 2061 2061 HOH HOH . P 4 HOH A 62 2062 2062 HOH HOH . P 4 HOH A 63 2063 2063 HOH HOH . P 4 HOH A 64 2064 2064 HOH HOH . P 4 HOH A 65 2065 2065 HOH HOH . P 4 HOH A 66 2066 2066 HOH HOH . P 4 HOH A 67 2067 2067 HOH HOH . P 4 HOH A 68 2068 2068 HOH HOH . P 4 HOH A 69 2069 2069 HOH HOH . P 4 HOH A 70 2070 2070 HOH HOH . P 4 HOH A 71 2071 2071 HOH HOH . P 4 HOH A 72 2072 2072 HOH HOH . P 4 HOH A 73 2073 2073 HOH HOH . P 4 HOH A 74 2074 2074 HOH HOH . P 4 HOH A 75 2075 2075 HOH HOH . P 4 HOH A 76 2076 2076 HOH HOH . P 4 HOH A 77 2077 2077 HOH HOH . P 4 HOH A 78 2078 2078 HOH HOH . P 4 HOH A 79 2079 2079 HOH HOH . P 4 HOH A 80 2080 2080 HOH HOH . P 4 HOH A 81 2081 2081 HOH HOH . P 4 HOH A 82 2082 2082 HOH HOH . P 4 HOH A 83 2083 2083 HOH HOH . P 4 HOH A 84 2084 2084 HOH HOH . P 4 HOH A 85 2085 2085 HOH HOH . P 4 HOH A 86 2086 2086 HOH HOH . P 4 HOH A 87 2087 2087 HOH HOH . P 4 HOH A 88 2088 2088 HOH HOH . P 4 HOH A 89 2089 2089 HOH HOH . P 4 HOH A 90 2090 2090 HOH HOH . P 4 HOH A 91 2091 2091 HOH HOH . P 4 HOH A 92 2092 2092 HOH HOH . P 4 HOH A 93 2093 2093 HOH HOH . P 4 HOH A 94 2094 2094 HOH HOH . P 4 HOH A 95 2095 2095 HOH HOH . P 4 HOH A 96 2096 2096 HOH HOH . P 4 HOH A 97 2097 2097 HOH HOH . P 4 HOH A 98 2098 2098 HOH HOH . P 4 HOH A 99 2099 2099 HOH HOH . P 4 HOH A 100 2100 2100 HOH HOH . P 4 HOH A 101 2101 2101 HOH HOH . P 4 HOH A 102 2102 2102 HOH HOH . P 4 HOH A 103 2103 2103 HOH HOH . P 4 HOH A 104 2104 2104 HOH HOH . P 4 HOH A 105 2105 2105 HOH HOH . P 4 HOH A 106 2106 2106 HOH HOH . P 4 HOH A 107 2107 2107 HOH HOH . P 4 HOH A 108 2108 2108 HOH HOH . P 4 HOH A 109 2109 2109 HOH HOH . P 4 HOH A 110 2110 2110 HOH HOH . P 4 HOH A 111 2111 2111 HOH HOH . P 4 HOH A 112 2112 2112 HOH HOH . P 4 HOH A 113 2113 2113 HOH HOH . P 4 HOH A 114 2114 2114 HOH HOH . P 4 HOH A 115 2115 2115 HOH HOH . P 4 HOH A 116 2116 2116 HOH HOH . P 4 HOH A 117 2117 2117 HOH HOH . P 4 HOH A 118 2118 2118 HOH HOH . P 4 HOH A 119 2119 2119 HOH HOH . P 4 HOH A 120 2120 2120 HOH HOH . P 4 HOH A 121 2121 2121 HOH HOH . P 4 HOH A 122 2122 2122 HOH HOH . Q 4 HOH B 1 2001 2001 HOH HOH . Q 4 HOH B 2 2002 2002 HOH HOH . Q 4 HOH B 3 2003 2003 HOH HOH . Q 4 HOH B 4 2004 2004 HOH HOH . Q 4 HOH B 5 2005 2005 HOH HOH . Q 4 HOH B 6 2006 2006 HOH HOH . Q 4 HOH B 7 2007 2007 HOH HOH . Q 4 HOH B 8 2008 2008 HOH HOH . Q 4 HOH B 9 2009 2009 HOH HOH . Q 4 HOH B 10 2010 2010 HOH HOH . Q 4 HOH B 11 2011 2011 HOH HOH . Q 4 HOH B 12 2012 2012 HOH HOH . Q 4 HOH B 13 2013 2013 HOH HOH . Q 4 HOH B 14 2014 2014 HOH HOH . Q 4 HOH B 15 2015 2015 HOH HOH . Q 4 HOH B 16 2016 2016 HOH HOH . Q 4 HOH B 17 2017 2017 HOH HOH . Q 4 HOH B 18 2018 2018 HOH HOH . Q 4 HOH B 19 2019 2019 HOH HOH . Q 4 HOH B 20 2020 2020 HOH HOH . Q 4 HOH B 21 2021 2021 HOH HOH . Q 4 HOH B 22 2022 2022 HOH HOH . Q 4 HOH B 23 2023 2023 HOH HOH . Q 4 HOH B 24 2024 2024 HOH HOH . Q 4 HOH B 25 2025 2025 HOH HOH . Q 4 HOH B 26 2026 2026 HOH HOH . Q 4 HOH B 27 2027 2027 HOH HOH . Q 4 HOH B 28 2028 2028 HOH HOH . Q 4 HOH B 29 2029 2029 HOH HOH . Q 4 HOH B 30 2030 2030 HOH HOH . Q 4 HOH B 31 2031 2031 HOH HOH . Q 4 HOH B 32 2032 2032 HOH HOH . Q 4 HOH B 33 2033 2033 HOH HOH . Q 4 HOH B 34 2034 2034 HOH HOH . Q 4 HOH B 35 2035 2035 HOH HOH . Q 4 HOH B 36 2036 2036 HOH HOH . Q 4 HOH B 37 2037 2037 HOH HOH . Q 4 HOH B 38 2038 2038 HOH HOH . Q 4 HOH B 39 2039 2039 HOH HOH . Q 4 HOH B 40 2040 2040 HOH HOH . Q 4 HOH B 41 2041 2041 HOH HOH . Q 4 HOH B 42 2042 2042 HOH HOH . Q 4 HOH B 43 2043 2043 HOH HOH . Q 4 HOH B 44 2044 2044 HOH HOH . Q 4 HOH B 45 2045 2045 HOH HOH . Q 4 HOH B 46 2046 2046 HOH HOH . Q 4 HOH B 47 2047 2047 HOH HOH . Q 4 HOH B 48 2048 2048 HOH HOH . Q 4 HOH B 49 2049 2049 HOH HOH . Q 4 HOH B 50 2050 2050 HOH HOH . Q 4 HOH B 51 2051 2051 HOH HOH . Q 4 HOH B 52 2052 2052 HOH HOH . Q 4 HOH B 53 2053 2053 HOH HOH . Q 4 HOH B 54 2054 2054 HOH HOH . Q 4 HOH B 55 2055 2055 HOH HOH . Q 4 HOH B 56 2056 2056 HOH HOH . Q 4 HOH B 57 2057 2057 HOH HOH . Q 4 HOH B 58 2058 2058 HOH HOH . Q 4 HOH B 59 2059 2059 HOH HOH . Q 4 HOH B 60 2060 2060 HOH HOH . Q 4 HOH B 61 2061 2061 HOH HOH . Q 4 HOH B 62 2062 2062 HOH HOH . Q 4 HOH B 63 2063 2063 HOH HOH . Q 4 HOH B 64 2064 2064 HOH HOH . Q 4 HOH B 65 2065 2065 HOH HOH . Q 4 HOH B 66 2066 2066 HOH HOH . Q 4 HOH B 67 2067 2067 HOH HOH . Q 4 HOH B 68 2068 2068 HOH HOH . Q 4 HOH B 69 2069 2069 HOH HOH . Q 4 HOH B 70 2070 2070 HOH HOH . Q 4 HOH B 71 2071 2071 HOH HOH . Q 4 HOH B 72 2072 2072 HOH HOH . Q 4 HOH B 73 2073 2073 HOH HOH . Q 4 HOH B 74 2074 2074 HOH HOH . Q 4 HOH B 75 2075 2075 HOH HOH . Q 4 HOH B 76 2076 2076 HOH HOH . Q 4 HOH B 77 2077 2077 HOH HOH . Q 4 HOH B 78 2078 2078 HOH HOH . Q 4 HOH B 79 2079 2079 HOH HOH . Q 4 HOH B 80 2080 2080 HOH HOH . Q 4 HOH B 81 2081 2081 HOH HOH . Q 4 HOH B 82 2082 2082 HOH HOH . Q 4 HOH B 83 2083 2083 HOH HOH . Q 4 HOH B 84 2084 2084 HOH HOH . Q 4 HOH B 85 2085 2085 HOH HOH . Q 4 HOH B 86 2086 2086 HOH HOH . Q 4 HOH B 87 2087 2087 HOH HOH . Q 4 HOH B 88 2088 2088 HOH HOH . Q 4 HOH B 89 2089 2089 HOH HOH . Q 4 HOH B 90 2090 2090 HOH HOH . Q 4 HOH B 91 2091 2091 HOH HOH . Q 4 HOH B 92 2092 2092 HOH HOH . Q 4 HOH B 93 2093 2093 HOH HOH . Q 4 HOH B 94 2094 2094 HOH HOH . Q 4 HOH B 95 2095 2095 HOH HOH . Q 4 HOH B 96 2096 2096 HOH HOH . Q 4 HOH B 97 2097 2097 HOH HOH . Q 4 HOH B 98 2098 2098 HOH HOH . Q 4 HOH B 99 2099 2099 HOH HOH . Q 4 HOH B 100 2100 2100 HOH HOH . Q 4 HOH B 101 2101 2101 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 I _atom_site.label_entity_id 3 _atom_site.Cartn_x 26.994 _atom_site.Cartn_y -10.122 _atom_site.Cartn_z 9.889 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 17.86 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 3504 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #