data_4D7Y # _model_server_result.job_id cpJi2Qq9xd5R6yuKib7ZvQ _model_server_result.datetime_utc '2024-11-05 00:58:01' _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 4d7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1261}' # _entry.id 4D7Y # _exptl.entry_id 4D7Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) 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 120 _cell.entry_id 4D7Y _cell.length_a 68.08 _cell.length_b 68.08 _cell.length_c 65.91 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D7Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -34.04 58.959009 0 3 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 34.04 58.959009 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E 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 OD2 ASP 72 A ASP 193 1_555 G MG MG . A MG 1264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc2 A OD2 ASP 87 A ASP 208 3_565 E NI NI . A NI 1262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc3 A OD2 ASP 87 A ASP 208 2_665 E NI NI . A NI 1262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc4 A OD2 ASP 87 A ASP 208 1_555 E NI NI . A NI 1262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc5 A OD1 ASP 89 A ASP 210 1_555 B CD CD . A CD 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc6 A OD2 ASP 89 A ASP 210 1_555 B CD CD . A CD 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc7 A OD1 ASP 89 A ASP 210 3_565 B CD CD . A CD 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc8 A OD2 ASP 89 A ASP 210 3_565 B CD CD . A CD 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc9 A OD2 ASP 89 A ASP 210 2_665 B CD CD . A CD 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc10 A OD1 ASP 89 A ASP 210 2_665 B CD CD . A CD 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc11 A OD1 ASP 93 A ASP 214 1_555 C CD CD . A CD 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc12 A OD1 ASP 93 A ASP 214 3_565 C CD CD . A CD 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc13 A OD1 ASP 93 A ASP 214 2_665 C CD CD . A CD 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc14 A OD2 ASP 93 A ASP 214 3_565 D NI NI . A NI 1261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc15 A OD2 ASP 93 A ASP 214 1_555 D NI NI . A NI 1261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc16 A OD2 ASP 93 A ASP 214 2_665 D NI NI . A NI 1261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc17 A OD2 ASP 114 A ASP 235 1_555 G MG MG . A MG 1264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc18 B CD CD . A CD 1259 1_555 F CL CL . A CL 1263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc19 B CD CD . A CD 1259 1_555 F CL CL . A CL 1263 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc20 B CD CD . A CD 1259 1_555 F CL CL . A CL 1263 3_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc21 C CD CD . A CD 1260 1_555 I O HOH . A HOH 2068 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc22 C CD CD . A CD 1260 1_555 I O HOH . A HOH 2068 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc23 C CD CD . A CD 1260 1_555 I O HOH . A HOH 2068 3_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc24 D NI NI . A NI 1261 1_555 I O HOH . A HOH 2063 3_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc25 D NI NI . A NI 1261 1_555 I O HOH . A HOH 2063 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc26 D NI NI . A NI 1261 1_555 I O HOH . A HOH 2063 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc27 E NI NI . A NI 1262 1_555 I O HOH . A HOH 2062 3_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc28 E NI NI . A NI 1262 1_555 I O HOH . A HOH 2062 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc29 E NI NI . A NI 1262 1_555 I O HOH . A HOH 2062 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc30 G MG MG . A MG 1264 1_555 I O HOH . A HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc31 G MG MG . A MG 1264 1_555 I O HOH . A HOH 2047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc32 G MG MG . A MG 1264 1_555 I O HOH . A HOH 2048 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? # _chem_comp.formula 'Ni 2' _chem_comp.formula_weight 58.693 _chem_comp.id NI _chem_comp.mon_nstd_flag . _chem_comp.name 'NICKEL (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4D7Y _atom_sites.fract_transf_matrix[1][1] 0.014689 _atom_sites.fract_transf_matrix[1][2] 0.00848 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016961 _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] 0.015172 _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 CD A 1 1259 1259 CD CD . C 2 CD A 1 1260 1260 CD CD . D 3 NI A 1 1261 1261 NI NI . E 3 NI A 1 1262 1262 NI NI . F 4 CL A 1 1263 1263 CL CL . G 5 MG A 1 1264 1264 MG MG . H 4 CL A 1 1265 1265 CL CL . I 6 HOH A 1 2001 2001 HOH HOH . I 6 HOH A 2 2002 2002 HOH HOH . I 6 HOH A 3 2003 2003 HOH HOH . I 6 HOH A 4 2004 2004 HOH HOH . I 6 HOH A 5 2005 2005 HOH HOH . I 6 HOH A 6 2006 2006 HOH HOH . I 6 HOH A 7 2007 2007 HOH HOH . I 6 HOH A 8 2008 2008 HOH HOH . I 6 HOH A 9 2009 2009 HOH HOH . I 6 HOH A 10 2010 2010 HOH HOH . I 6 HOH A 11 2011 2011 HOH HOH . I 6 HOH A 12 2012 2012 HOH HOH . I 6 HOH A 13 2013 2013 HOH HOH . I 6 HOH A 14 2014 2014 HOH HOH . I 6 HOH A 15 2015 2015 HOH HOH . I 6 HOH A 16 2016 2016 HOH HOH . I 6 HOH A 17 2017 2017 HOH HOH . I 6 HOH A 18 2018 2018 HOH HOH . I 6 HOH A 19 2019 2019 HOH HOH . I 6 HOH A 20 2020 2020 HOH HOH . I 6 HOH A 21 2021 2021 HOH HOH . I 6 HOH A 22 2022 2022 HOH HOH . I 6 HOH A 23 2023 2023 HOH HOH . I 6 HOH A 24 2024 2024 HOH HOH . I 6 HOH A 25 2025 2025 HOH HOH . I 6 HOH A 26 2026 2026 HOH HOH . I 6 HOH A 27 2027 2027 HOH HOH . I 6 HOH A 28 2028 2028 HOH HOH . I 6 HOH A 29 2029 2029 HOH HOH . I 6 HOH A 30 2030 2030 HOH HOH . I 6 HOH A 31 2031 2031 HOH HOH . I 6 HOH A 32 2032 2032 HOH HOH . I 6 HOH A 33 2033 2033 HOH HOH . I 6 HOH A 34 2034 2034 HOH HOH . I 6 HOH A 35 2035 2035 HOH HOH . I 6 HOH A 36 2036 2036 HOH HOH . I 6 HOH A 37 2037 2037 HOH HOH . I 6 HOH A 38 2038 2038 HOH HOH . I 6 HOH A 39 2039 2039 HOH HOH . I 6 HOH A 40 2040 2040 HOH HOH . I 6 HOH A 41 2041 2041 HOH HOH . I 6 HOH A 42 2042 2042 HOH HOH . I 6 HOH A 43 2043 2043 HOH HOH . I 6 HOH A 44 2044 2044 HOH HOH . I 6 HOH A 45 2045 2045 HOH HOH . I 6 HOH A 46 2046 2046 HOH HOH . I 6 HOH A 47 2047 2047 HOH HOH . I 6 HOH A 48 2048 2048 HOH HOH . I 6 HOH A 49 2049 2049 HOH HOH . I 6 HOH A 50 2050 2050 HOH HOH . I 6 HOH A 51 2051 2051 HOH HOH . I 6 HOH A 52 2052 2052 HOH HOH . I 6 HOH A 53 2053 2053 HOH HOH . I 6 HOH A 54 2054 2054 HOH HOH . I 6 HOH A 55 2055 2055 HOH HOH . I 6 HOH A 56 2056 2056 HOH HOH . I 6 HOH A 57 2057 2057 HOH HOH . I 6 HOH A 58 2058 2058 HOH HOH . I 6 HOH A 59 2059 2059 HOH HOH . I 6 HOH A 60 2060 2060 HOH HOH . I 6 HOH A 61 2061 2061 HOH HOH . I 6 HOH A 62 2062 2062 HOH HOH . I 6 HOH A 63 2063 2063 HOH HOH . I 6 HOH A 64 2064 2064 HOH HOH . I 6 HOH A 65 2065 2065 HOH HOH . I 6 HOH A 66 2066 2066 HOH HOH . I 6 HOH A 67 2067 2067 HOH HOH . I 6 HOH A 68 2068 2068 HOH HOH . I 6 HOH A 69 2069 2069 HOH HOH . I 6 HOH A 70 2070 2070 HOH HOH . I 6 HOH A 71 2071 2071 HOH HOH . I 6 HOH A 72 2072 2072 HOH HOH . I 6 HOH A 73 2073 2073 HOH HOH . I 6 HOH A 74 2074 2074 HOH HOH . I 6 HOH A 75 2075 2075 HOH HOH . I 6 HOH A 76 2076 2076 HOH HOH . I 6 HOH A 77 2077 2077 HOH HOH . I 6 HOH A 78 2078 2078 HOH HOH . I 6 HOH A 79 2079 2079 HOH HOH . I 6 HOH A 80 2080 2080 HOH HOH . I 6 HOH A 81 2081 2081 HOH HOH . I 6 HOH A 82 2082 2082 HOH HOH . I 6 HOH A 83 2083 2083 HOH HOH . I 6 HOH A 84 2084 2084 HOH HOH . I 6 HOH A 85 2085 2085 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NI _atom_site.label_atom_id NI _atom_site.label_comp_id NI _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 3 _atom_site.Cartn_x 0 _atom_site.Cartn_y 39.306 _atom_site.Cartn_z 23.696 _atom_site.occupancy 0.36 _atom_site.B_iso_or_equiv 8.62 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 1261 _atom_site.auth_asym_id A _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 2 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #