data_4CDW # _model_server_result.job_id ZRO2xL3fnQqho6a31ChjRA _model_server_result.datetime_utc '2024-10-12 23:22:11' _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 4cdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1243}' # _entry.id 4CDW # _exptl.entry_id 4CDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 6 _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 4CDW _cell.length_a 599.66 _cell.length_b 599.66 _cell.length_c 599.66 _cell.Z_PDB 480 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CDW _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 33.81624 289.28274 3 'point symmetry operation' ? ? -0.488171 -0.594263 0.639171 -0.769034 0.639171 0.006909 -0.412645 -0.488171 -0.769034 211.30972 164.41283 390.89546 4 'point symmetry operation' ? ? -0.488171 -0.769034 -0.412645 -0.594263 0.639171 -0.488171 0.639171 0.006909 -0.769034 390.89546 211.30972 164.41283 5 'point symmetry operation' ? ? 0.431569 -0.401759 -0.807675 -0.118975 0.862176 -0.492441 0.8942 0.308615 0.324289 260.29887 109.69701 -77.17385 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 323.09898 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 33.81624 8 'point symmetry operation' ? ? 0.30953 0.735914 -0.60218 -0.759166 0.57259 0.30953 0.57259 0.361346 0.735914 81.5123 128.40919 -98.07343 9 'point symmetry operation' ? ? 0.324289 0.8942 0.308615 -0.807675 0.431569 -0.401759 -0.492441 -0.118975 0.862176 -77.17385 260.29887 109.69701 10 'point symmetry operation' ? ? -0.46856 0.5804 0.666024 -0.197464 0.666024 -0.71932 -0.861081 -0.46856 -0.197464 32.52316 183.12502 369.99587 11 'point symmetry operation' ? ? 0.951945 -0.204295 0.228176 -0.204295 -0.978618 -0.023881 0.228176 -0.023881 -0.973327 3.53928 323.09898 259.00579 12 'point symmetry operation' ? ? 0.308615 -0.401759 0.862176 0.324289 -0.807675 -0.492441 0.8942 0.431569 -0.118975 33.81624 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 260.29887 109.69701 -77.17385 14 'point symmetry operation' ? ? -0.197464 -0.861081 -0.46856 0.666024 -0.46856 0.5804 -0.71932 -0.197464 0.666024 369.99587 32.52316 183.12502 15 'point symmetry operation' ? ? 0.639171 -0.488171 -0.594263 0.006909 -0.769034 0.639171 -0.769034 -0.412645 -0.488171 211.30972 164.41283 390.89546 16 'point symmetry operation' ? ? -0.978618 -0.023881 -0.204295 -0.023881 -0.973327 0.228176 -0.204295 0.228176 0.951945 323.09898 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 183.12502 369.99587 19 'point symmetry operation' ? ? 0.361346 0.735914 0.57259 0.735914 -0.60218 0.30953 0.57259 0.30953 -0.759166 -98.07343 81.5123 128.40919 20 'point symmetry operation' ? ? -0.60218 0.30953 0.735914 0.30953 -0.759166 0.57259 0.735914 0.57259 0.361346 81.5123 128.40919 -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 323.09898 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 369.99587 32.52316 183.12502 24 'point symmetry operation' ? ? 0.57259 0.30953 -0.759166 0.361346 0.735914 0.57259 0.735914 -0.60218 0.30953 128.40919 -98.07343 81.5123 25 'point symmetry operation' ? ? 0.735914 0.57259 0.361346 -0.60218 0.30953 0.735914 0.30953 -0.759166 0.57259 -98.07343 81.5123 128.40919 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 323.09898 27 'point symmetry operation' ? ? 0.8942 0.431569 -0.118975 0.308615 -0.401759 0.862176 0.324289 -0.807675 -0.492441 -30.27695 33.81624 289.28274 28 'point symmetry operation' ? ? 0.308615 0.324289 0.8942 -0.401759 -0.807675 0.431569 0.862176 -0.492441 -0.118975 -77.17385 260.29887 109.69701 29 'point symmetry operation' ? ? -0.71932 -0.197464 0.666024 -0.197464 -0.861081 -0.46856 0.666024 -0.46856 0.5804 183.12502 369.99587 32.52316 30 'point symmetry operation' ? ? -0.769034 -0.412645 -0.488171 0.639171 -0.488171 -0.594263 0.006909 -0.769034 0.639171 390.89546 211.30972 164.41283 31 'point symmetry operation' ? ? -0.023881 -0.204295 -0.978618 -0.973327 0.228176 -0.023881 0.228176 0.951945 -0.204295 323.09898 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 33.81624 289.28274 -30.27695 33 'point symmetry operation' ? ? 0.57259 0.361346 0.735914 0.30953 0.735914 -0.60218 -0.759166 0.57259 0.30953 -98.07343 81.5123 128.40919 34 'point symmetry operation' ? ? -0.492441 -0.118975 0.862176 0.324289 0.8942 0.308615 -0.807675 0.431569 -0.401759 109.69701 -77.17385 260.29887 35 'point symmetry operation' ? ? -0.861081 -0.46856 -0.197464 -0.46856 0.5804 0.666024 -0.197464 0.666024 -0.71932 369.99587 32.52316 183.12502 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 33.81624 38 'point symmetry operation' ? ? -0.412645 -0.488171 -0.769034 -0.488171 -0.594263 0.639171 -0.769034 0.639171 0.006909 390.89546 211.30972 164.41283 39 'point symmetry operation' ? ? 0.639171 0.006909 -0.769034 -0.488171 -0.769034 -0.412645 -0.594263 0.639171 -0.488171 164.41283 390.89546 211.30972 40 'point symmetry operation' ? ? 0.8942 0.308615 0.324289 0.431569 -0.401759 -0.807675 -0.118975 0.862176 -0.492441 -77.17385 260.29887 109.69701 41 'point symmetry operation' ? ? -0.204295 -0.978618 -0.023881 0.228176 -0.023881 -0.973327 0.951945 -0.204295 0.228176 323.09898 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 33.81624 43 'point symmetry operation' ? ? 0.862176 -0.492441 -0.118975 0.308615 0.324289 0.8942 -0.401759 -0.807675 0.431569 109.69701 -77.17385 260.29887 44 'point symmetry operation' ? ? 0.666024 -0.46856 0.5804 -0.71932 -0.197464 0.666024 -0.197464 -0.861081 -0.46856 32.52316 183.12502 369.99587 45 'point symmetry operation' ? ? 0.006909 -0.769034 0.639171 -0.769034 -0.412645 -0.488171 0.639171 -0.488171 -0.594263 164.41283 390.89546 211.30972 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 323.09898 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 183.12502 369.99587 32.52316 49 'point symmetry operation' ? ? 0.735914 -0.60218 0.30953 0.57259 0.30953 -0.759166 0.361346 0.735914 0.57259 81.5123 128.40919 -98.07343 50 'point symmetry operation' ? ? 0.30953 -0.759166 0.57259 0.735914 0.57259 0.361346 -0.60218 0.30953 0.735914 128.40919 -98.07343 81.5123 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 33.81624 289.28274 -30.27695 53 'point symmetry operation' ? ? -0.769034 0.639171 0.006909 -0.412645 -0.488171 -0.769034 -0.488171 -0.594263 0.639171 164.41283 390.89546 211.30972 54 'point symmetry operation' ? ? -0.594263 0.639171 -0.488171 0.639171 0.006909 -0.769034 -0.488171 -0.769034 -0.412645 211.30972 164.41283 390.89546 55 'point symmetry operation' ? ? -0.118975 0.862176 -0.492441 0.8942 0.308615 0.324289 0.431569 -0.401759 -0.807675 109.69701 -77.17385 260.29887 56 'point symmetry operation' ? ? 0.228176 0.951945 -0.204295 -0.023881 -0.204295 -0.978618 -0.973327 0.228176 -0.023881 3.53928 323.09898 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 33.81624 289.28274 58 'point symmetry operation' ? ? -0.759166 0.57259 0.30953 0.57259 0.361346 0.735914 0.30953 0.735914 -0.60218 128.40919 -98.07343 81.5123 59 'point symmetry operation' ? ? -0.807675 0.431569 -0.401759 -0.492441 -0.118975 0.862176 0.324289 0.8942 0.308615 260.29887 109.69701 -77.17385 60 'point symmetry operation' ? ? -0.197464 0.666024 -0.71932 -0.861081 -0.46856 -0.197464 -0.46856 0.5804 0.666024 183.12502 369.99587 32.52316 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 G N N # _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 4CDW _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 VR2 A 1 1298 1298 VR2 VR2 . F 6 NA C 1 1243 1243 NA NA . G 6 NA C 1 1244 1244 NA NA . H 7 HOH A 1 2001 2001 HOH HOH . H 7 HOH A 2 2002 2002 HOH HOH . H 7 HOH A 3 2003 2003 HOH HOH . H 7 HOH A 4 2004 2004 HOH HOH . H 7 HOH A 5 2005 2005 HOH HOH . H 7 HOH A 6 2006 2006 HOH HOH . H 7 HOH A 7 2007 2007 HOH HOH . H 7 HOH A 8 2008 2008 HOH HOH . H 7 HOH A 9 2009 2009 HOH HOH . H 7 HOH A 10 2010 2010 HOH HOH . H 7 HOH A 11 2011 2011 HOH HOH . H 7 HOH A 12 2012 2012 HOH HOH . H 7 HOH A 13 2013 2013 HOH HOH . H 7 HOH A 14 2014 2014 HOH HOH . H 7 HOH A 15 2015 2015 HOH HOH . H 7 HOH A 16 2016 2016 HOH HOH . H 7 HOH A 17 2017 2017 HOH HOH . H 7 HOH A 18 2018 2018 HOH HOH . H 7 HOH A 19 2019 2019 HOH HOH . H 7 HOH A 20 2020 2020 HOH HOH . H 7 HOH A 21 2021 2021 HOH HOH . H 7 HOH A 22 2022 2022 HOH HOH . H 7 HOH A 23 2023 2023 HOH HOH . H 7 HOH A 24 2024 2024 HOH HOH . I 7 HOH B 1 2001 2001 HOH HOH . I 7 HOH B 2 2002 2002 HOH HOH . I 7 HOH B 3 2003 2003 HOH HOH . I 7 HOH B 4 2004 2004 HOH HOH . I 7 HOH B 5 2005 2005 HOH HOH . I 7 HOH B 6 2006 2006 HOH HOH . I 7 HOH B 7 2007 2007 HOH HOH . I 7 HOH B 8 2008 2008 HOH HOH . I 7 HOH B 9 2009 2009 HOH HOH . I 7 HOH B 10 2010 2010 HOH HOH . I 7 HOH B 11 2011 2011 HOH HOH . I 7 HOH B 12 2012 2012 HOH HOH . I 7 HOH B 13 2013 2013 HOH HOH . I 7 HOH B 14 2014 2014 HOH HOH . J 7 HOH C 1 2001 2001 HOH HOH . J 7 HOH C 2 2002 2002 HOH HOH . J 7 HOH C 3 2003 2003 HOH HOH . J 7 HOH C 4 2004 2004 HOH HOH . J 7 HOH C 5 2005 2005 HOH HOH . J 7 HOH C 6 2006 2006 HOH HOH . J 7 HOH C 7 2007 2007 HOH HOH . J 7 HOH C 8 2008 2008 HOH HOH . J 7 HOH C 9 2009 2009 HOH HOH . J 7 HOH C 10 2010 2010 HOH HOH . J 7 HOH C 11 2011 2011 HOH HOH . J 7 HOH C 12 2012 2012 HOH HOH . J 7 HOH C 13 2013 2013 HOH HOH . J 7 HOH C 14 2014 2014 HOH HOH . K 7 HOH D 1 2001 2001 HOH HOH . K 7 HOH D 2 2003 2003 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 F _atom_site.label_entity_id 6 _atom_site.Cartn_x 93.749 _atom_site.Cartn_y 259.721 _atom_site.Cartn_z 140.893 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 29.17 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1243 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 1 #