data_1WVC # _model_server_result.job_id Ea4XoNy-JdU5y_4f-3CWnQ _model_server_result.datetime_utc '2025-04-26 20:19:42' _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 1wvc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":403}' # _entry.id 1WVC # _exptl.entry_id 1WVC _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 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 1WVC _cell.length_a 84.2 _cell.length_b 84.2 _cell.length_c 157.4 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WVC _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 42.1 72.919339 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -42.1 72.919339 0 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 42.1 72.919339 78.7 5 'crystal symmetry operation' 11_555 -x+y,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 78.7 6 'crystal symmetry operation' 12_565 x,x-y+1,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -42.1 72.919339 78.7 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 NE2 HIS 79 A HIS 79 1_555 C NI NI . A NI 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc2 A OD2 ASP 131 A ASP 131 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc3 A OD1 ASP 236 A ASP 236 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc4 E O2A CTP . A CTP 401 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc5 E O1A CTP . A CTP 401 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.101 ? metalc ? metalc6 E O1G CTP . A CTP 401 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? metalc ? metalc7 E O3A CTP . A CTP 401 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? # _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 1WVC _atom_sites.fract_transf_matrix[1][1] 0.011876 _atom_sites.fract_transf_matrix[1][2] 0.006857 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013714 _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] 0.006353 _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 MG A 1 402 402 MG MG . C 3 NI A 1 403 403 NI NI . D 2 MG A 1 501 501 MG MG . E 4 CTP A 1 401 401 CTP CTP . F 5 HOH A 1 701 701 HOH HOH . F 5 HOH A 2 705 705 HOH HOH . F 5 HOH A 3 707 707 HOH HOH . F 5 HOH A 4 708 708 HOH HOH . F 5 HOH A 5 713 713 HOH HOH . F 5 HOH A 6 714 714 HOH HOH . F 5 HOH A 7 901 901 HOH HOH . F 5 HOH A 8 902 902 HOH HOH . F 5 HOH A 9 1101 1101 HOH HOH . F 5 HOH A 10 1102 1102 HOH HOH . F 5 HOH A 11 1103 1103 HOH HOH . F 5 HOH A 12 1104 1104 HOH HOH . F 5 HOH A 13 1106 1106 HOH HOH . F 5 HOH A 14 1107 1107 HOH HOH . F 5 HOH A 15 1108 1108 HOH HOH . F 5 HOH A 16 1109 1109 HOH HOH . F 5 HOH A 17 1112 1112 HOH HOH . F 5 HOH A 18 1114 1114 HOH HOH . F 5 HOH A 19 1117 1117 HOH HOH . F 5 HOH A 20 1124 1124 HOH HOH . F 5 HOH A 21 1126 1126 HOH HOH . F 5 HOH A 22 1300 1300 HOH HOH . F 5 HOH A 23 1303 1303 HOH HOH . F 5 HOH A 24 1310 1310 HOH HOH . F 5 HOH A 25 1311 1311 HOH HOH . F 5 HOH A 26 1312 1312 HOH HOH . F 5 HOH A 27 1313 1313 HOH HOH . F 5 HOH A 28 1315 1315 HOH HOH . F 5 HOH A 29 1316 1316 HOH HOH . F 5 HOH A 30 1317 1317 HOH HOH . F 5 HOH A 31 1324 1324 HOH HOH . F 5 HOH A 32 1325 1325 HOH HOH . F 5 HOH A 33 1500 1500 HOH HOH . F 5 HOH A 34 1501 1501 HOH HOH . F 5 HOH A 35 1502 1502 HOH HOH . F 5 HOH A 36 1503 1503 HOH HOH . F 5 HOH A 37 1504 1504 HOH HOH . F 5 HOH A 38 1512 1512 HOH HOH . F 5 HOH A 39 1515 1515 HOH HOH . F 5 HOH A 40 1516 1516 HOH HOH . F 5 HOH A 41 1517 1517 HOH HOH . F 5 HOH A 42 1701 1701 HOH HOH . F 5 HOH A 43 1703 1703 HOH HOH . F 5 HOH A 44 1704 1704 HOH HOH . F 5 HOH A 45 1705 1705 HOH HOH . F 5 HOH A 46 1706 1706 HOH HOH . F 5 HOH A 47 1901 1901 HOH HOH . F 5 HOH A 48 1902 1902 HOH HOH . F 5 HOH A 49 1905 1905 HOH HOH . F 5 HOH A 50 1906 1906 HOH HOH . F 5 HOH A 51 1907 1907 HOH HOH . F 5 HOH A 52 1908 1908 HOH HOH . F 5 HOH A 53 1910 1910 HOH HOH . F 5 HOH A 54 1911 1911 HOH HOH . F 5 HOH A 55 1912 1912 HOH HOH . F 5 HOH A 56 1913 1913 HOH HOH . F 5 HOH A 57 1914 1914 HOH HOH . F 5 HOH A 58 2100 2100 HOH HOH . F 5 HOH A 59 2101 2101 HOH HOH . F 5 HOH A 60 2103 2103 HOH HOH . F 5 HOH A 61 2105 2105 HOH HOH . F 5 HOH A 62 2107 2107 HOH HOH . F 5 HOH A 63 2109 2109 HOH HOH . F 5 HOH A 64 2110 2110 HOH HOH . F 5 HOH A 65 2111 2111 HOH HOH . F 5 HOH A 66 2112 2112 HOH HOH . F 5 HOH A 67 2113 2113 HOH HOH . F 5 HOH A 68 2114 2114 HOH HOH . F 5 HOH A 69 2115 2115 HOH HOH . F 5 HOH A 70 2118 2118 HOH HOH . F 5 HOH A 71 2120 2120 HOH HOH . F 5 HOH A 72 2121 2121 HOH HOH . F 5 HOH A 73 2300 2300 HOH HOH . F 5 HOH A 74 2301 2301 HOH HOH . F 5 HOH A 75 2302 2302 HOH HOH . F 5 HOH A 76 2303 2303 HOH HOH . F 5 HOH A 77 2304 2304 HOH HOH . F 5 HOH A 78 2305 2305 HOH HOH . F 5 HOH A 79 2308 2308 HOH HOH . F 5 HOH A 80 2309 2309 HOH HOH . F 5 HOH A 81 2310 2310 HOH HOH . F 5 HOH A 82 2311 2311 HOH HOH . F 5 HOH A 83 2500 2500 HOH HOH . F 5 HOH A 84 2502 2502 HOH HOH . F 5 HOH A 85 2505 2505 HOH HOH . F 5 HOH A 86 2506 2506 HOH HOH . F 5 HOH A 87 2507 2507 HOH HOH . F 5 HOH A 88 2512 2512 HOH HOH . F 5 HOH A 89 2513 2513 HOH HOH . F 5 HOH A 90 2514 2514 HOH HOH . F 5 HOH A 91 2515 2515 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 C _atom_site.label_entity_id 3 _atom_site.Cartn_x -8.992 _atom_site.Cartn_y 64.397 _atom_site.Cartn_z 78.859 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 58.44 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 403 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 491 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #