data_4CDU # _model_server_result.job_id iYBzRQTI6PlUp3IeLxeApA _model_server_result.datetime_utc '2024-10-12 23:24:06' _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 4cdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1070}' # _entry.id 4CDU # _exptl.entry_id 4CDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 7 _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 4CDU _cell.length_a 599.681 _cell.length_b 599.681 _cell.length_c 599.681 _cell.Z_PDB 480 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 240-MERIC 240 'complete icosahedral assembly' 1 ? tetrameric 4 'icosahedral asymmetric unit' 2 ? eicosameric 20 'icosahedral pentamer' 3 ? 24-meric 24 'icosahedral 23 hexamer' 4 ? tetrameric 4 'icosahedral asymmetric unit, std point frame' 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K 1 (1-60) A,B,C,D,E,F,G,H,I,J,K 2 1 A,B,C,D,E,F,G,H,I,J,K 3 (1-5) A,B,C,D,E,F,G,H,I,J,K 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H,I,J,K 5 P # 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] P 'transform to point frame' ? ? 0.103397 -0.115484 -0.987913 -0.987913 0.103397 -0.115484 0.115484 0.987913 -0.103397 146.41101 146.41101 -146.41101 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.431569 -0.118975 0.8942 -0.401759 0.862176 0.308615 -0.807675 -0.492441 0.324289 -30.27695 33.81623 289.28274 3 'point symmetry operation' ? ? -0.488171 -0.594264 0.639171 -0.769034 0.639171 0.006909 -0.412645 -0.488171 -0.769034 211.30973 164.41282 390.89545 4 'point symmetry operation' ? ? -0.488171 -0.769034 -0.412645 -0.594264 0.639171 -0.488171 0.639171 0.006909 -0.769034 390.89545 211.30973 164.41282 5 'point symmetry operation' ? ? 0.431569 -0.401759 -0.807675 -0.118975 0.862176 -0.492441 0.8942 0.308615 0.324289 260.29886 109.69702 -77.17386 6 'point symmetry operation' ? ? -0.973327 0.228176 -0.023881 0.228176 0.951945 -0.204295 -0.023881 -0.204295 -0.978618 259.00579 3.53928 323.09897 7 'point symmetry operation' ? ? -0.492441 0.324289 -0.807675 -0.118975 0.8942 0.431569 0.862176 0.308615 -0.401759 289.28274 -30.27695 33.81623 8 'point symmetry operation' ? ? 0.30953 0.735915 -0.60218 -0.759166 0.57259 0.30953 0.57259 0.361346 0.735915 81.51229 128.4092 -98.07343 9 'point symmetry operation' ? ? 0.324289 0.8942 0.308615 -0.807675 0.431569 -0.401759 -0.492441 -0.118975 0.862176 -77.17386 260.29886 109.69702 10 'point symmetry operation' ? ? -0.46856 0.5804 0.666024 -0.197464 0.666024 -0.71932 -0.861081 -0.46856 -0.197464 32.52316 183.125 369.99588 11 'point symmetry operation' ? ? 0.951945 -0.204295 0.228176 -0.204295 -0.978618 -0.023881 0.228176 -0.023881 -0.973327 3.53928 323.09897 259.00579 12 'point symmetry operation' ? ? 0.308615 -0.401759 0.862176 0.324289 -0.807675 -0.492441 0.8942 0.431569 -0.118975 33.81623 289.28274 -30.27695 13 'point symmetry operation' ? ? -0.401759 -0.807675 0.431569 0.862176 -0.492441 -0.118975 0.308615 0.324289 0.8942 260.29886 109.69702 -77.17386 14 'point symmetry operation' ? ? -0.197464 -0.861081 -0.46856 0.666024 -0.46856 0.5804 -0.71932 -0.197464 0.666024 369.99588 32.52316 183.125 15 'point symmetry operation' ? ? 0.639171 -0.488171 -0.594264 0.006909 -0.769034 0.639171 -0.769034 -0.412645 -0.488171 211.30973 164.41282 390.89545 16 'point symmetry operation' ? ? -0.978618 -0.023881 -0.204295 -0.023881 -0.973327 0.228176 -0.204295 0.228176 0.951945 323.09897 259.00579 3.53928 17 'point symmetry operation' ? ? -0.247743 0.196444 -0.948701 0.196444 -0.948701 -0.247743 -0.948701 -0.247743 0.196444 292.82202 292.82202 292.82202 18 'point symmetry operation' ? ? 0.5804 0.666024 -0.46856 0.666024 -0.71932 -0.197464 -0.46856 -0.197464 -0.861081 32.52316 183.125 369.99588 19 'point symmetry operation' ? ? 0.361346 0.735915 0.57259 0.735915 -0.60218 0.30953 0.57259 0.30953 -0.759166 -98.07343 81.51229 128.4092 20 'point symmetry operation' ? ? -0.60218 0.30953 0.735915 0.30953 -0.759166 0.57259 0.735915 0.57259 0.361346 81.51229 128.4092 -98.07343 21 'point symmetry operation' ? ? -0.204295 0.228176 0.951945 -0.978618 -0.023881 -0.204295 -0.023881 -0.973327 0.228176 3.53928 323.09897 259.00579 22 'point symmetry operation' ? ? -0.948701 -0.247743 0.196444 -0.247743 0.196444 -0.948701 0.196444 -0.948701 -0.247743 292.82202 292.82202 292.82202 23 'point symmetry operation' ? ? -0.46856 -0.197464 -0.861081 0.5804 0.666024 -0.46856 0.666024 -0.71932 -0.197464 369.99588 32.52316 183.125 24 'point symmetry operation' ? ? 0.57259 0.30953 -0.759166 0.361346 0.735915 0.57259 0.735915 -0.60218 0.30953 128.4092 -98.07343 81.51229 25 'point symmetry operation' ? ? 0.735915 0.57259 0.361346 -0.60218 0.30953 0.735915 0.30953 -0.759166 0.57259 -98.07343 81.51229 128.4092 26 'point symmetry operation' ? ? 0.228176 -0.023881 -0.973327 0.951945 -0.204295 0.228176 -0.204295 -0.978618 -0.023881 259.00579 3.53928 323.09897 27 'point symmetry operation' ? ? 0.8942 0.431569 -0.118975 0.308615 -0.401759 0.862176 0.324289 -0.807675 -0.492441 -30.27695 33.81623 289.28274 28 'point symmetry operation' ? ? 0.308615 0.324289 0.8942 -0.401759 -0.807675 0.431569 0.862176 -0.492441 -0.118975 -77.17386 260.29886 109.69702 29 'point symmetry operation' ? ? -0.71932 -0.197464 0.666024 -0.197464 -0.861081 -0.46856 0.666024 -0.46856 0.5804 183.125 369.99588 32.52316 30 'point symmetry operation' ? ? -0.769034 -0.412645 -0.488171 0.639171 -0.488171 -0.594264 0.006909 -0.769034 0.639171 390.89545 211.30973 164.41282 31 'point symmetry operation' ? ? -0.023881 -0.204295 -0.978618 -0.973327 0.228176 -0.023881 0.228176 0.951945 -0.204295 323.09897 259.00579 3.53928 32 'point symmetry operation' ? ? 0.862176 0.308615 -0.401759 -0.492441 0.324289 -0.807675 -0.118975 0.8942 0.431569 33.81623 289.28274 -30.27695 33 'point symmetry operation' ? ? 0.57259 0.361346 0.735915 0.30953 0.735915 -0.60218 -0.759166 0.57259 0.30953 -98.07343 81.51229 128.4092 34 'point symmetry operation' ? ? -0.492441 -0.118975 0.862176 0.324289 0.8942 0.308615 -0.807675 0.431569 -0.401759 109.69702 -77.17386 260.29886 35 'point symmetry operation' ? ? -0.861081 -0.46856 -0.197464 -0.46856 0.5804 0.666024 -0.197464 0.666024 -0.71932 369.99588 32.52316 183.125 36 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 37 'point symmetry operation' ? ? -0.807675 -0.492441 0.324289 0.431569 -0.118975 0.8942 -0.401759 0.862176 0.308615 289.28274 -30.27695 33.81623 38 'point symmetry operation' ? ? -0.412645 -0.488171 -0.769034 -0.488171 -0.594264 0.639171 -0.769034 0.639171 0.006909 390.89545 211.30973 164.41282 39 'point symmetry operation' ? ? 0.639171 0.006909 -0.769034 -0.488171 -0.769034 -0.412645 -0.594264 0.639171 -0.488171 164.41282 390.89545 211.30973 40 'point symmetry operation' ? ? 0.8942 0.308615 0.324289 0.431569 -0.401759 -0.807675 -0.118975 0.862176 -0.492441 -77.17386 260.29886 109.69702 41 'point symmetry operation' ? ? -0.204295 -0.978618 -0.023881 0.228176 -0.023881 -0.973327 0.951945 -0.204295 0.228176 323.09897 259.00579 3.53928 42 'point symmetry operation' ? ? 0.324289 -0.807675 -0.492441 0.8942 0.431569 -0.118975 0.308615 -0.401759 0.862176 289.28274 -30.27695 33.81623 43 'point symmetry operation' ? ? 0.862176 -0.492441 -0.118975 0.308615 0.324289 0.8942 -0.401759 -0.807675 0.431569 109.69702 -77.17386 260.29886 44 'point symmetry operation' ? ? 0.666024 -0.46856 0.5804 -0.71932 -0.197464 0.666024 -0.197464 -0.861081 -0.46856 32.52316 183.125 369.99588 45 'point symmetry operation' ? ? 0.006909 -0.769034 0.639171 -0.769034 -0.412645 -0.488171 0.639171 -0.488171 -0.594264 164.41282 390.89545 211.30973 46 'point symmetry operation' ? ? -0.023881 -0.973327 0.228176 -0.204295 0.228176 0.951945 -0.978618 -0.023881 -0.204295 259.00579 3.53928 323.09897 47 'point symmetry operation' ? ? 0.196444 -0.948701 -0.247743 -0.948701 -0.247743 0.196444 -0.247743 0.196444 -0.948701 292.82202 292.82202 292.82202 48 'point symmetry operation' ? ? 0.666024 -0.71932 -0.197464 -0.46856 -0.197464 -0.861081 0.5804 0.666024 -0.46856 183.125 369.99588 32.52316 49 'point symmetry operation' ? ? 0.735915 -0.60218 0.30953 0.57259 0.30953 -0.759166 0.361346 0.735915 0.57259 81.51229 128.4092 -98.07343 50 'point symmetry operation' ? ? 0.30953 -0.759166 0.57259 0.735915 0.57259 0.361346 -0.60218 0.30953 0.735915 128.4092 -98.07343 81.51229 51 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 0 52 'point symmetry operation' ? ? -0.401759 0.862176 0.308615 -0.807675 -0.492441 0.324289 0.431569 -0.118975 0.8942 33.81623 289.28274 -30.27695 53 'point symmetry operation' ? ? -0.769034 0.639171 0.006909 -0.412645 -0.488171 -0.769034 -0.488171 -0.594264 0.639171 164.41282 390.89545 211.30973 54 'point symmetry operation' ? ? -0.594264 0.639171 -0.488171 0.639171 0.006909 -0.769034 -0.488171 -0.769034 -0.412645 211.30973 164.41282 390.89545 55 'point symmetry operation' ? ? -0.118975 0.862176 -0.492441 0.8942 0.308615 0.324289 0.431569 -0.401759 -0.807675 109.69702 -77.17386 260.29886 56 'point symmetry operation' ? ? 0.228176 0.951945 -0.204295 -0.023881 -0.204295 -0.978618 -0.973327 0.228176 -0.023881 3.53928 323.09897 259.00579 57 'point symmetry operation' ? ? -0.118975 0.8942 0.431569 0.862176 0.308615 -0.401759 -0.492441 0.324289 -0.807675 -30.27695 33.81623 289.28274 58 'point symmetry operation' ? ? -0.759166 0.57259 0.30953 0.57259 0.361346 0.735915 0.30953 0.735915 -0.60218 128.4092 -98.07343 81.51229 59 'point symmetry operation' ? ? -0.807675 0.431569 -0.401759 -0.492441 -0.118975 0.862176 0.324289 0.8942 0.308615 260.29886 109.69702 -77.17386 60 'point symmetry operation' ? ? -0.197464 0.666024 -0.71932 -0.861081 -0.46856 -0.197464 -0.46856 0.5804 0.666024 183.125 369.99588 32.52316 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 G N N ? 7 H N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id D _struct_conn.ptnr1_label_atom_id OD2 _struct_conn.ptnr1_label_comp_id ASP _struct_conn.ptnr1_label_seq_id 35 _struct_conn.ptnr1_auth_asym_id D _struct_conn.ptnr1_auth_comp_id ASP _struct_conn.ptnr1_auth_seq_id 35 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id H _struct_conn.ptnr2_label_atom_id NA _struct_conn.ptnr2_label_comp_id NA _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id D _struct_conn.ptnr2_auth_comp_id NA _struct_conn.ptnr2_auth_seq_id 1070 _struct_conn.ptnr2_symmetry 1_555 _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 3.024 _struct_conn.pdbx_value_order ? # _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 4CDU _atom_sites.fract_transf_matrix[1][1] 0.001668 _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] 0.001668 _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] 0.001668 _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 YM2 A 1 1298 1298 YM2 YM2 . F 6 CL B 1 1255 1255 CL CL . G 7 NA C 1 1243 1243 NA NA . H 7 NA D 1 1070 1070 NA NA . I 8 HOH A 1 2001 2001 HOH HOH . I 8 HOH A 2 2002 2002 HOH HOH . I 8 HOH A 3 2003 2003 HOH HOH . I 8 HOH A 4 2004 2004 HOH HOH . I 8 HOH A 5 2005 2005 HOH HOH . I 8 HOH A 6 2006 2006 HOH HOH . I 8 HOH A 7 2007 2007 HOH HOH . I 8 HOH A 8 2008 2008 HOH HOH . I 8 HOH A 9 2009 2009 HOH HOH . I 8 HOH A 10 2010 2010 HOH HOH . I 8 HOH A 11 2011 2011 HOH HOH . I 8 HOH A 12 2012 2012 HOH HOH . I 8 HOH A 13 2013 2013 HOH HOH . I 8 HOH A 14 2014 2014 HOH HOH . I 8 HOH A 15 2015 2015 HOH HOH . I 8 HOH A 16 2016 2016 HOH HOH . I 8 HOH A 17 2017 2017 HOH HOH . I 8 HOH A 18 2018 2018 HOH HOH . I 8 HOH A 19 2019 2019 HOH HOH . I 8 HOH A 20 2020 2020 HOH HOH . I 8 HOH A 21 2021 2021 HOH HOH . I 8 HOH A 22 2022 2022 HOH HOH . I 8 HOH A 23 2023 2023 HOH HOH . I 8 HOH A 24 2024 2024 HOH HOH . I 8 HOH A 25 2025 2025 HOH HOH . I 8 HOH A 26 2026 2026 HOH HOH . J 8 HOH B 1 2001 2001 HOH HOH . J 8 HOH B 2 2002 2002 HOH HOH . J 8 HOH B 3 2003 2003 HOH HOH . J 8 HOH B 4 2004 2004 HOH HOH . J 8 HOH B 5 2005 2005 HOH HOH . J 8 HOH B 6 2006 2006 HOH HOH . J 8 HOH B 7 2007 2007 HOH HOH . J 8 HOH B 8 2008 2008 HOH HOH . J 8 HOH B 9 2009 2009 HOH HOH . J 8 HOH B 10 2010 2010 HOH HOH . J 8 HOH B 11 2011 2011 HOH HOH . J 8 HOH B 12 2012 2012 HOH HOH . J 8 HOH B 13 2013 2013 HOH HOH . J 8 HOH B 14 2014 2014 HOH HOH . J 8 HOH B 15 2015 2015 HOH HOH . J 8 HOH B 16 2016 2016 HOH HOH . J 8 HOH B 17 2017 2017 HOH HOH . J 8 HOH B 18 2018 2018 HOH HOH . J 8 HOH B 19 2019 2019 HOH HOH . J 8 HOH B 20 2020 2020 HOH HOH . J 8 HOH B 21 2021 2021 HOH HOH . J 8 HOH B 22 2022 2022 HOH HOH . K 8 HOH C 1 2001 2001 HOH HOH . K 8 HOH C 2 2002 2002 HOH HOH . K 8 HOH C 3 2003 2003 HOH HOH . K 8 HOH C 4 2004 2004 HOH HOH . K 8 HOH C 5 2005 2005 HOH HOH . K 8 HOH C 6 2006 2006 HOH HOH . K 8 HOH C 7 2007 2007 HOH HOH . K 8 HOH C 8 2008 2008 HOH HOH . K 8 HOH C 9 2009 2009 HOH HOH . K 8 HOH C 10 2010 2010 HOH HOH . K 8 HOH C 11 2011 2011 HOH HOH . K 8 HOH C 12 2012 2012 HOH HOH . K 8 HOH C 13 2013 2013 HOH HOH . K 8 HOH C 14 2014 2014 HOH HOH . K 8 HOH C 15 2015 2015 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 H _atom_site.label_entity_id 7 _atom_site.Cartn_x 96.945 _atom_site.Cartn_y 249.012 _atom_site.Cartn_z 109.356 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 27.93 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1070 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 1 #