data_2Z5R # _model_server_result.job_id r5DWzsPo9gjpoq-KCSbGug _model_server_result.datetime_utc '2024-12-12 06:29:34' _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 2z5r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 2Z5R # _exptl.entry_id 2Z5R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 106.42 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PALLADIUM ION' _entity.pdbx_number_of_molecules 10 _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 2Z5R _cell.length_a 181.594 _cell.length_b 181.594 _cell.length_c 181.594 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Z5R _symmetry.cell_setting ? _symmetry.Int_Tables_number 209 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'F 4 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 6 'crystal symmetry operation' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 7 'crystal symmetry operation' 7_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 8 'crystal symmetry operation' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 9 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 10 'crystal symmetry operation' 10_555 -y,z,-x 0 -1 0 0 0 1 -1 0 0 0 0 0 11 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 12 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 13 'crystal symmetry operation' 13_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 14 'crystal symmetry operation' 14_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 15 'crystal symmetry operation' 15_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 16 'crystal symmetry operation' 16_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 17 'crystal symmetry operation' 17_555 x,z,-y 1 0 0 0 0 1 0 -1 0 0 0 0 18 'crystal symmetry operation' 18_555 -x,z,y -1 0 0 0 0 1 0 1 0 0 0 0 19 'crystal symmetry operation' 19_555 -x,-z,-y -1 0 0 0 0 -1 0 -1 0 0 0 0 20 'crystal symmetry operation' 20_555 x,-z,y 1 0 0 0 0 -1 0 1 0 0 0 0 21 'crystal symmetry operation' 21_555 z,y,-x 0 0 1 0 1 0 -1 0 0 0 0 0 22 'crystal symmetry operation' 22_555 z,-y,x 0 0 1 0 -1 0 1 0 0 0 0 0 23 'crystal symmetry operation' 23_555 -z,y,x 0 0 -1 0 1 0 1 0 0 0 0 0 24 'crystal symmetry operation' 24_555 -z,-y,-x 0 0 -1 0 -1 0 -1 0 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K 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 OE1 GLU 60 A GLU 60 1_555 M CD CD . A CD 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc2 A NH1 ARG 64 A ARG 64 1_555 K PD PD . A PD 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc3 A OD1 ASP 80 A ASP 80 1_555 L CD CD . A CD 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc4 A OD2 ASP 80 A ASP 80 1_555 L CD CD . A CD 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 A NE2 HIS 114 A HIS 114 1_555 F PD PD . A PD 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc6 A NE2 HIS 124 A HIS 124 1_555 D PD PD . A PD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc7 A OE1 GLU 136 A GLU 136 1_555 K PD PD . A PD 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? # _chem_comp.formula 'Pd 2' _chem_comp.formula_weight 106.42 _chem_comp.id PD _chem_comp.mon_nstd_flag . _chem_comp.name 'PALLADIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2Z5R _atom_sites.fract_transf_matrix[1][1] 0.005507 _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] 0.005507 _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] 0.005507 _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 PD A 1 201 201 PD PD . C 2 PD A 1 202 202 PD PD . D 2 PD A 1 203 203 PD PD . E 2 PD A 1 204 204 PD PD . F 2 PD A 1 205 205 PD PD . G 2 PD A 1 206 206 PD PD . H 2 PD A 1 207 207 PD PD . I 2 PD A 1 208 208 PD PD . J 2 PD A 1 209 209 PD PD . K 2 PD A 1 210 210 PD PD . L 3 CD A 1 211 211 CD CD . M 3 CD A 1 212 212 CD CD . N 4 HOH A 1 1001 1001 HOH HOH . N 4 HOH A 2 1002 1002 HOH HOH . N 4 HOH A 3 1003 1003 HOH HOH . N 4 HOH A 4 1004 1004 HOH HOH . N 4 HOH A 5 1005 1005 HOH HOH . N 4 HOH A 6 1006 1006 HOH HOH . N 4 HOH A 7 1007 1007 HOH HOH . N 4 HOH A 8 1008 1008 HOH HOH . N 4 HOH A 9 1009 1009 HOH HOH . N 4 HOH A 10 1010 1010 HOH HOH . N 4 HOH A 11 1011 1011 HOH HOH . N 4 HOH A 12 1012 1012 HOH HOH . N 4 HOH A 13 1013 1013 HOH HOH . N 4 HOH A 14 1014 1014 HOH HOH . N 4 HOH A 15 1015 1015 HOH HOH . N 4 HOH A 16 1016 1016 HOH HOH . N 4 HOH A 17 1017 1017 HOH HOH . N 4 HOH A 18 1018 1018 HOH HOH . N 4 HOH A 19 1019 1019 HOH HOH . N 4 HOH A 20 1020 1020 HOH HOH . N 4 HOH A 21 1021 1021 HOH HOH . N 4 HOH A 22 1022 1022 HOH HOH . N 4 HOH A 23 1023 1023 HOH HOH . N 4 HOH A 24 1024 1024 HOH HOH . N 4 HOH A 25 1025 1025 HOH HOH . N 4 HOH A 26 1026 1026 HOH HOH . N 4 HOH A 27 1027 1027 HOH HOH . N 4 HOH A 28 1028 1028 HOH HOH . N 4 HOH A 29 1029 1029 HOH HOH . N 4 HOH A 30 1030 1030 HOH HOH . N 4 HOH A 31 1031 1031 HOH HOH . N 4 HOH A 32 1032 1032 HOH HOH . N 4 HOH A 33 1033 1033 HOH HOH . N 4 HOH A 34 1034 1034 HOH HOH . N 4 HOH A 35 1035 1035 HOH HOH . N 4 HOH A 36 1036 1036 HOH HOH . N 4 HOH A 37 1037 1037 HOH HOH . N 4 HOH A 38 1038 1038 HOH HOH . N 4 HOH A 39 1039 1039 HOH HOH . N 4 HOH A 40 1040 1040 HOH HOH . N 4 HOH A 41 1041 1041 HOH HOH . N 4 HOH A 42 1042 1042 HOH HOH . N 4 HOH A 43 1043 1043 HOH HOH . N 4 HOH A 44 1044 1044 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol PD _atom_site.label_atom_id PD _atom_site.label_comp_id PD _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 2 _atom_site.Cartn_x -36.838 _atom_site.Cartn_y -24.581 _atom_site.Cartn_z -20.592 _atom_site.occupancy 0.5 _atom_site.B_iso_or_equiv 56.69 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id PD _atom_site.auth_comp_id PD _atom_site.auth_seq_id 203 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 1 #