data_6DK8 # _model_server_result.job_id bJIp5FInZa7IFzuPK5nsHg _model_server_result.datetime_utc '2024-10-19 14:37:37' _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 6dk8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":701}' # _entry.id 6DK8 # _exptl.entry_id 6DK8 _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 20 _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 6DK8 _cell.length_a 158.708 _cell.length_b 158.708 _cell.length_c 243.826 _cell.Z_PDB 64 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DK8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K,L,M,N 1 1 C,D,O,P,Q,R 2 1 E,F,S,T,U,V,W 3 1 G,H,X,Y,Z,AA,BA 4 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X N N ? 2 Y N N ? 2 Z N N ? 2 AA N N ? 2 BA 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 NE2 HIS 9 A HIS 424 1_555 J NI NI . A NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc2 A OE2 GLU 23 A GLU 438 1_555 K NI NI . A NI 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc3 A NE2 HIS 42 A HIS 457 1_555 K NI NI . A NI 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc4 A ND1 HIS 176 A HIS 591 1_555 I NI NI . A NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc5 A NE2 HIS 176 A HIS 591 1_555 I NI NI . A NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc6 J NI NI . A NI 702 1_555 B NE2 HIS 189 B HIS 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc7 B ND1 HIS 9 B HIS 424 1_555 L NI NI . B NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc8 B OE2 GLU 23 B GLU 438 1_555 M NI NI . B NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc9 B NE2 HIS 42 B HIS 457 1_555 M NI NI . B NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc10 B NE2 HIS 160 B HIS 575 1_555 N NI NI . B NI 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc11 B OD1 ASP 163 B ASP 578 1_555 N NI NI . B NI 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc12 C NE2 HIS 9 C HIS 424 1_555 O NI NI . C NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc13 C NE2 HIS 160 C HIS 575 1_555 P NI NI . C NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc14 C NE2 HIS 176 C HIS 591 1_555 Q NI NI . C NI 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc15 O NI NI . C NI 701 1_555 D NE2 HIS 189 D HIS 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc16 P NI NI . C NI 702 1_555 E NE2 HIS 160 E HIS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc17 D OE2 GLU 23 D GLU 438 1_555 R NI NI . D NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? metalc ? metalc18 D NE2 HIS 42 D HIS 457 1_555 R NI NI . D NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc19 E NE2 HIS 9 E HIS 424 1_555 U NI NI . E NI 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc20 E NE2 HIS 42 E HIS 457 1_555 T NI NI . E NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc21 E NE2 HIS 176 E HIS 591 1_555 S NI NI . E NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc22 S NI NI . E NI 701 1_555 F NE2 HIS 176 F HIS 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc23 U NI NI . E NI 703 1_555 F NE2 HIS 189 F HIS 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc24 F OE2 GLU 23 F GLU 438 1_555 W NI NI . F NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc25 F NE2 HIS 42 F HIS 457 1_555 W NI NI . F NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc26 G NE2 HIS 9 G HIS 424 1_555 Y NI NI . G NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc27 G NE2 HIS 42 G HIS 457 1_555 Z NI NI . G NI 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc28 G ND1 HIS 176 G HIS 591 1_555 AA NI NI . H NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc29 Y NI NI . G NI 702 1_555 H NE2 HIS 189 H HIS 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc30 H OE2 GLU 23 H GLU 438 1_555 BA NI NI . H NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc31 H NE2 HIS 42 H HIS 457 1_555 BA NI NI . H NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc32 H ND1 HIS 176 H HIS 591 1_555 AA NI NI . H NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc33 H NE2 HIS 176 H HIS 591 1_555 AA NI NI . H NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? # _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 6DK8 _atom_sites.fract_transf_matrix[1][1] 0.006301 _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] 0.006301 _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] 0.004101 _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 I 2 NI A 1 701 2 NI NI . J 2 NI A 1 702 12 NI NI . K 2 NI A 1 703 17 NI NI . L 2 NI B 1 701 3 NI NI . M 2 NI B 1 702 19 NI NI . N 2 NI B 1 703 20 NI NI . O 2 NI C 1 701 4 NI NI . P 2 NI C 1 702 5 NI NI . Q 2 NI C 1 703 6 NI NI . R 2 NI D 1 701 13 NI NI . S 2 NI E 1 701 8 NI NI . T 2 NI E 1 702 14 NI NI . U 2 NI E 1 703 21 NI NI . V 2 NI F 1 701 9 NI NI . W 2 NI F 1 702 15 NI NI . X 2 NI G 1 701 1 NI NI . Y 2 NI G 1 702 10 NI NI . Z 2 NI G 1 703 16 NI NI . AA 2 NI H 1 701 11 NI NI . BA 2 NI H 1 702 18 NI NI . # _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 AA _atom_site.label_entity_id 2 _atom_site.Cartn_x -15.724 _atom_site.Cartn_y 2.321 _atom_site.Cartn_z 31.79 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 66.34 _atom_site.pdbx_formal_charge 2 _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 701 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 115 _model_server_stats.parse_time_ms 147 _model_server_stats.create_model_time_ms 130 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #