data_5Y9R # _model_server_result.job_id CYKvI8wAc6U0pF0BXs1PqQ _model_server_result.datetime_utc '2025-09-11 14:26:34' _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 5y9r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5Y9R # _exptl.entry_id 5Y9R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 2 _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 90 _cell.entry_id 5Y9R _cell.length_a 51.12 _cell.length_b 57.43 _cell.length_c 62.6 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y9R _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,C,D,G,H,I,J,K,M,N,O 1 1 A,E,F,L 1 2 # 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_545 -x,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 -28.715 31.3 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 H 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 32 A GLU 125 1_555 G CD CD . B CD 201 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? metalc ? metalc2 A NE2 HIS 38 A HIS 131 1_555 E NI NI . A NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc3 E NI NI . A NI 201 3_545 B OE1 GLU 29 B GLU 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc4 E NI NI . A NI 201 3_545 B OE1 GLU 32 B GLU 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc5 E NI NI . A NI 201 1_555 M O HOH . B HOH 305 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc6 E NI NI . A NI 201 1_555 M O HOH . B HOH 306 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc7 E NI NI . A NI 201 1_555 M O HOH . B HOH 312 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc8 L O HOH . A HOH 308 3_545 G CD CD . B CD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc9 B OD2 ASP 21 B ASP 114 1_555 G CD CD . B CD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc10 B NE2 HIS 38 B HIS 131 1_555 H NI NI . B NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc11 G CD CD . B CD 201 1_555 C NE2 HIS 38 D HIS 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc12 H NI NI . B NI 202 1_555 C OD1 ASP 21 D ASP 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc13 H NI NI . B NI 202 1_555 C OD2 ASP 21 D ASP 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc14 H NI NI . B NI 202 1_555 N O HOH . D HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? # _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 5Y9R _atom_sites.fract_transf_matrix[1][1] 0.019562 _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] 0.017413 _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] 0.015974 _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 2 NI A 1 201 2 NI NI . F 3 EDO A 1 202 2 EDO EDO . G 4 CD B 1 201 1 CD CD . H 2 NI B 1 202 1 NI NI . I 3 EDO D 1 201 4 EDO EDO . J 3 EDO C 1 201 1 EDO EDO . K 3 EDO C 1 202 3 EDO EDO . L 5 HOH A 1 301 34 HOH HOH . L 5 HOH A 2 302 15 HOH HOH . L 5 HOH A 3 303 4 HOH HOH . L 5 HOH A 4 304 52 HOH HOH . L 5 HOH A 5 305 5 HOH HOH . L 5 HOH A 6 306 38 HOH HOH . L 5 HOH A 7 307 20 HOH HOH . L 5 HOH A 8 308 53 HOH HOH . L 5 HOH A 9 309 36 HOH HOH . M 5 HOH B 1 301 1 HOH HOH . M 5 HOH B 2 302 26 HOH HOH . M 5 HOH B 3 303 54 HOH HOH . M 5 HOH B 4 304 61 HOH HOH . M 5 HOH B 5 305 60 HOH HOH . M 5 HOH B 6 306 58 HOH HOH . M 5 HOH B 7 307 62 HOH HOH . M 5 HOH B 8 308 56 HOH HOH . M 5 HOH B 9 309 6 HOH HOH . M 5 HOH B 10 310 10 HOH HOH . M 5 HOH B 11 311 29 HOH HOH . M 5 HOH B 12 312 59 HOH HOH . M 5 HOH B 13 313 21 HOH HOH . M 5 HOH B 14 314 63 HOH HOH . M 5 HOH B 15 315 13 HOH HOH . M 5 HOH B 16 316 65 HOH HOH . N 5 HOH D 1 301 46 HOH HOH . N 5 HOH D 2 302 32 HOH HOH . N 5 HOH D 3 303 11 HOH HOH . N 5 HOH D 4 304 25 HOH HOH . N 5 HOH D 5 305 9 HOH HOH . N 5 HOH D 6 306 3 HOH HOH . N 5 HOH D 7 307 42 HOH HOH . N 5 HOH D 8 308 14 HOH HOH . N 5 HOH D 9 309 27 HOH HOH . O 5 HOH C 1 301 43 HOH HOH . O 5 HOH C 2 302 8 HOH HOH . O 5 HOH C 3 303 44 HOH HOH . O 5 HOH C 4 304 12 HOH HOH . O 5 HOH C 5 305 64 HOH HOH . O 5 HOH C 6 306 55 HOH HOH . O 5 HOH C 7 307 57 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 E _atom_site.label_entity_id 2 _atom_site.Cartn_x 3.593 _atom_site.Cartn_y 90.857 _atom_site.Cartn_z 15.94 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 37.25 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 201 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #