data_1JMO # _model_server_result.job_id WLel9fpF0aOXu756hBBE0Q _model_server_result.datetime_utc '2024-12-11 23:07:31' _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 1jmo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 1JMO # _exptl.entry_id 1JMO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 1JMO _cell.length_a 152.31 _cell.length_b 152.31 _cell.length_c 126.8 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JMO _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K,L,M,N,O _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 B 1 NAG X 1 NAG 4 n D NAG 2 B 2 NAG X 2 NAG # 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 disulf ? disulf1 A SG CYS 22 L CYS 1 1_555 B SG CYS 120 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 B SG CYS 29 H CYS 42 1_555 B SG CYS 45 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 B SG CYS 174 H CYS 168 1_555 B SG CYS 188 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 202 H CYS 191 1_555 B SG CYS 232 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? covale ? covale1 B ND2 ASN 54 H ASN 60 1_555 D C1 NAG . B NAG 1 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 C C ASP 59 A ASP 59 1_555 C N TYS 60 A TYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 C C TYS 60 A TYS 60 1_555 C N LEU 61 A LEU 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale4 C C ASP 72 A ASP 72 1_555 C N TYS 73 A TYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 C C TYS 73 A TYS 73 1_555 C N ILE 74 A ILE 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 C ND2 ASN 169 A ASN 169 1_555 H C1 NAG . A NAG 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 C ND2 ASN 368 A ASN 368 1_555 I C1 NAG . A NAG 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale8 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? metalc ? metalc1 B O LYS 237 H LYS 224 1_555 E NA NA . H NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc2 E NA NA . H NA 501 1_555 N O HOH . H HOH 2048 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? # _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 1JMO _atom_sites.fract_transf_matrix[1][1] 0.006566 _atom_sites.fract_transf_matrix[1][2] 0.003791 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007581 _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] 0.007886 _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 E 5 NA H 1 501 501 NA NA . F 6 MPD H 1 2003 2003 MPD MPD . G 6 MPD H 1 2004 2004 MPD MPD . H 7 NAG A 1 481 1 NAG NAG . I 7 NAG A 1 482 1 NAG NAG . J 6 MPD A 1 2001 2001 MPD MPD . K 6 MPD A 1 2002 2002 MPD MPD . L 6 MPD A 1 2005 2005 MPD MPD . M 8 HOH L 1 15 5 HOH HOH . M 8 HOH L 2 16 6 HOH HOH . M 8 HOH L 3 17 25 HOH HOH . M 8 HOH L 4 18 34 HOH HOH . M 8 HOH L 5 19 37 HOH HOH . M 8 HOH L 6 20 39 HOH HOH . M 8 HOH L 7 21 40 HOH HOH . M 8 HOH L 8 22 45 HOH HOH . M 8 HOH L 9 23 48 HOH HOH . M 8 HOH L 10 24 61 HOH HOH . M 8 HOH L 11 25 62 HOH HOH . M 8 HOH L 12 26 77 HOH HOH . M 8 HOH L 13 27 79 HOH HOH . M 8 HOH L 14 28 81 HOH HOH . M 8 HOH L 15 29 90 HOH HOH . M 8 HOH L 16 30 94 HOH HOH . M 8 HOH L 17 31 97 HOH HOH . M 8 HOH L 18 32 101 HOH HOH . M 8 HOH L 19 33 103 HOH HOH . M 8 HOH L 20 34 104 HOH HOH . M 8 HOH L 21 35 108 HOH HOH . M 8 HOH L 22 36 110 HOH HOH . M 8 HOH L 23 37 111 HOH HOH . M 8 HOH L 24 38 112 HOH HOH . M 8 HOH L 25 39 113 HOH HOH . M 8 HOH L 26 40 122 HOH HOH . M 8 HOH L 27 41 123 HOH HOH . M 8 HOH L 28 42 124 HOH HOH . M 8 HOH L 29 43 125 HOH HOH . M 8 HOH L 30 44 126 HOH HOH . M 8 HOH L 31 45 143 HOH HOH . M 8 HOH L 32 46 144 HOH HOH . M 8 HOH L 33 47 167 HOH HOH . M 8 HOH L 34 48 168 HOH HOH . M 8 HOH L 35 49 169 HOH HOH . M 8 HOH L 36 50 170 HOH HOH . M 8 HOH L 37 51 171 HOH HOH . M 8 HOH L 38 52 172 HOH HOH . M 8 HOH L 39 53 175 HOH HOH . N 8 HOH H 1 2005 1 HOH HOH . N 8 HOH H 2 2006 2 HOH HOH . N 8 HOH H 3 2007 3 HOH HOH . N 8 HOH H 4 2008 4 HOH HOH . N 8 HOH H 5 2009 7 HOH HOH . N 8 HOH H 6 2010 8 HOH HOH . N 8 HOH H 7 2011 9 HOH HOH . N 8 HOH H 8 2012 10 HOH HOH . N 8 HOH H 9 2013 11 HOH HOH . N 8 HOH H 10 2014 12 HOH HOH . N 8 HOH H 11 2015 13 HOH HOH . N 8 HOH H 12 2016 14 HOH HOH . N 8 HOH H 13 2017 15 HOH HOH . N 8 HOH H 14 2018 16 HOH HOH . N 8 HOH H 15 2019 17 HOH HOH . N 8 HOH H 16 2020 18 HOH HOH . N 8 HOH H 17 2021 19 HOH HOH . N 8 HOH H 18 2022 20 HOH HOH . N 8 HOH H 19 2023 27 HOH HOH . N 8 HOH H 20 2024 28 HOH HOH . N 8 HOH H 21 2025 30 HOH HOH . N 8 HOH H 22 2026 32 HOH HOH . N 8 HOH H 23 2027 41 HOH HOH . N 8 HOH H 24 2028 42 HOH HOH . N 8 HOH H 25 2029 43 HOH HOH . N 8 HOH H 26 2030 49 HOH HOH . N 8 HOH H 27 2031 50 HOH HOH . N 8 HOH H 28 2032 52 HOH HOH . N 8 HOH H 29 2033 53 HOH HOH . N 8 HOH H 30 2034 54 HOH HOH . N 8 HOH H 31 2035 55 HOH HOH . N 8 HOH H 32 2036 56 HOH HOH . N 8 HOH H 33 2037 57 HOH HOH . N 8 HOH H 34 2038 58 HOH HOH . N 8 HOH H 35 2039 65 HOH HOH . N 8 HOH H 36 2040 66 HOH HOH . N 8 HOH H 37 2041 71 HOH HOH . N 8 HOH H 38 2042 74 HOH HOH . N 8 HOH H 39 2043 84 HOH HOH . N 8 HOH H 40 2044 85 HOH HOH . N 8 HOH H 41 2045 88 HOH HOH . N 8 HOH H 42 2046 91 HOH HOH . N 8 HOH H 43 2047 93 HOH HOH . N 8 HOH H 44 2048 98 HOH HOH . N 8 HOH H 45 2049 99 HOH HOH . N 8 HOH H 46 2050 102 HOH HOH . N 8 HOH H 47 2051 105 HOH HOH . N 8 HOH H 48 2052 107 HOH HOH . N 8 HOH H 49 2053 114 HOH HOH . N 8 HOH H 50 2054 127 HOH HOH . N 8 HOH H 51 2055 128 HOH HOH . N 8 HOH H 52 2056 129 HOH HOH . N 8 HOH H 53 2057 130 HOH HOH . N 8 HOH H 54 2058 131 HOH HOH . N 8 HOH H 55 2059 132 HOH HOH . N 8 HOH H 56 2060 133 HOH HOH . N 8 HOH H 57 2061 134 HOH HOH . N 8 HOH H 58 2062 135 HOH HOH . N 8 HOH H 59 2063 136 HOH HOH . N 8 HOH H 60 2064 141 HOH HOH . N 8 HOH H 61 2065 142 HOH HOH . N 8 HOH H 62 2066 145 HOH HOH . N 8 HOH H 63 2067 146 HOH HOH . N 8 HOH H 64 2068 147 HOH HOH . N 8 HOH H 65 2069 148 HOH HOH . N 8 HOH H 66 2070 150 HOH HOH . N 8 HOH H 67 2071 151 HOH HOH . N 8 HOH H 68 2072 152 HOH HOH . N 8 HOH H 69 2073 153 HOH HOH . N 8 HOH H 70 2074 173 HOH HOH . N 8 HOH H 71 2075 174 HOH HOH . N 8 HOH H 72 2076 176 HOH HOH . N 8 HOH H 73 2077 179 HOH HOH . N 8 HOH H 74 2078 180 HOH HOH . N 8 HOH H 75 2079 181 HOH HOH . N 8 HOH H 76 2080 182 HOH HOH . N 8 HOH H 77 2081 183 HOH HOH . N 8 HOH H 78 2082 184 HOH HOH . N 8 HOH H 79 2083 185 HOH HOH . N 8 HOH H 80 2084 186 HOH HOH . N 8 HOH H 81 2085 187 HOH HOH . N 8 HOH H 82 2086 188 HOH HOH . N 8 HOH H 83 2087 189 HOH HOH . O 8 HOH A 1 2006 21 HOH HOH . O 8 HOH A 2 2007 22 HOH HOH . O 8 HOH A 3 2008 23 HOH HOH . O 8 HOH A 4 2009 24 HOH HOH . O 8 HOH A 5 2010 26 HOH HOH . O 8 HOH A 6 2011 29 HOH HOH . O 8 HOH A 7 2012 31 HOH HOH . O 8 HOH A 8 2013 33 HOH HOH . O 8 HOH A 9 2014 35 HOH HOH . O 8 HOH A 10 2015 36 HOH HOH . O 8 HOH A 11 2016 38 HOH HOH . O 8 HOH A 12 2017 44 HOH HOH . O 8 HOH A 13 2018 46 HOH HOH . O 8 HOH A 14 2019 47 HOH HOH . O 8 HOH A 15 2020 51 HOH HOH . O 8 HOH A 16 2021 59 HOH HOH . O 8 HOH A 17 2022 60 HOH HOH . O 8 HOH A 18 2023 63 HOH HOH . O 8 HOH A 19 2024 64 HOH HOH . O 8 HOH A 20 2025 67 HOH HOH . O 8 HOH A 21 2026 68 HOH HOH . O 8 HOH A 22 2027 69 HOH HOH . O 8 HOH A 23 2028 70 HOH HOH . O 8 HOH A 24 2029 72 HOH HOH . O 8 HOH A 25 2030 73 HOH HOH . O 8 HOH A 26 2031 75 HOH HOH . O 8 HOH A 27 2032 76 HOH HOH . O 8 HOH A 28 2033 78 HOH HOH . O 8 HOH A 29 2034 80 HOH HOH . O 8 HOH A 30 2035 82 HOH HOH . O 8 HOH A 31 2036 83 HOH HOH . O 8 HOH A 32 2037 86 HOH HOH . O 8 HOH A 33 2038 87 HOH HOH . O 8 HOH A 34 2039 89 HOH HOH . O 8 HOH A 35 2040 92 HOH HOH . O 8 HOH A 36 2041 95 HOH HOH . O 8 HOH A 37 2042 96 HOH HOH . O 8 HOH A 38 2043 100 HOH HOH . O 8 HOH A 39 2044 106 HOH HOH . O 8 HOH A 40 2045 109 HOH HOH . O 8 HOH A 41 2046 115 HOH HOH . O 8 HOH A 42 2047 116 HOH HOH . O 8 HOH A 43 2048 117 HOH HOH . O 8 HOH A 44 2049 118 HOH HOH . O 8 HOH A 45 2050 119 HOH HOH . O 8 HOH A 46 2051 120 HOH HOH . O 8 HOH A 47 2052 121 HOH HOH . O 8 HOH A 48 2053 137 HOH HOH . O 8 HOH A 49 2054 138 HOH HOH . O 8 HOH A 50 2055 139 HOH HOH . O 8 HOH A 51 2056 140 HOH HOH . O 8 HOH A 52 2057 149 HOH HOH . O 8 HOH A 53 2058 154 HOH HOH . O 8 HOH A 54 2059 155 HOH HOH . O 8 HOH A 55 2060 156 HOH HOH . O 8 HOH A 56 2061 157 HOH HOH . O 8 HOH A 57 2062 158 HOH HOH . O 8 HOH A 58 2063 159 HOH HOH . O 8 HOH A 59 2064 160 HOH HOH . O 8 HOH A 60 2065 161 HOH HOH . O 8 HOH A 61 2066 162 HOH HOH . O 8 HOH A 62 2067 163 HOH HOH . O 8 HOH A 63 2068 164 HOH HOH . O 8 HOH A 64 2069 165 HOH HOH . O 8 HOH A 65 2070 166 HOH HOH . O 8 HOH A 66 2071 177 HOH HOH . O 8 HOH A 67 2072 178 HOH HOH . O 8 HOH A 68 2073 190 HOH HOH . O 8 HOH A 69 2074 191 HOH HOH . O 8 HOH A 70 2075 192 HOH HOH . O 8 HOH A 71 2076 193 HOH HOH . O 8 HOH A 72 2077 194 HOH HOH . O 8 HOH A 73 2078 195 HOH HOH . O 8 HOH A 74 2079 196 HOH HOH . O 8 HOH A 75 2080 197 HOH HOH . O 8 HOH A 76 2081 198 HOH HOH . O 8 HOH A 77 2082 199 HOH HOH . O 8 HOH A 78 2083 200 HOH HOH . O 8 HOH A 79 2084 201 HOH HOH . O 8 HOH A 80 2085 202 HOH HOH . O 8 HOH A 81 2086 203 HOH HOH . O 8 HOH A 82 2087 204 HOH HOH . O 8 HOH A 83 2088 205 HOH HOH . O 8 HOH A 84 2089 206 HOH HOH . O 8 HOH A 85 2090 207 HOH HOH . O 8 HOH A 86 2091 208 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 E _atom_site.label_entity_id 5 _atom_site.Cartn_x 75.227 _atom_site.Cartn_y 56.714 _atom_site.Cartn_z 133.552 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 67.06 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 501 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #