data_6JFD # _model_server_result.job_id d5O-oOo1w3GA6GzgX_yfwg _model_server_result.datetime_utc '2024-10-10 08:23:17' _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 6jfd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":201}' # _entry.id 6JFD # _exptl.entry_id 6JFD _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.9 _cell.angle_gamma 90 _cell.entry_id 6JFD _cell.length_a 44.33 _cell.length_b 146.356 _cell.length_c 65.306 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JFD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 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,E,L 1 1 B,F,G,M 2 1 C,H,I,N 3 1 D,J,K,O 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 E N N ? 2 F N N ? 2 G N N ? 2 H 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 SG CYS 100 A CYS 103 1_555 E NI NI . A NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc2 A NE2 HIS 142 A HIS 145 1_555 E NI NI . A NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc3 A NE2 HIS 146 A HIS 149 1_555 E NI NI . A NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc4 B OE2 GLU 22 B GLU 25 1_555 G NI NI . B NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc5 B OE2 GLU 28 B GLU 31 1_555 K NI NI . D NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc6 B SG CYS 100 B CYS 103 1_555 F NI NI . B NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc7 B NE2 HIS 142 B HIS 145 1_555 F NI NI . B NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc8 B NE2 HIS 146 B HIS 149 1_555 F NI NI . B NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc9 G NI NI . B NI 202 1_555 D OE2 GLU 28 D GLU 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc10 C SG CYS 100 C CYS 103 1_555 H NI NI . C NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc11 C NE2 HIS 142 C HIS 145 1_555 H NI NI . C NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc12 C NE2 HIS 146 C HIS 149 1_555 H NI NI . C NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc13 H NI NI . C NI 201 1_555 I O2 K1U . C K1U 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc14 D OE2 GLU 22 D GLU 25 1_555 K NI NI . D NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc15 D SG CYS 100 D CYS 103 1_555 J NI NI . D NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc16 D NE2 HIS 142 D HIS 145 1_555 J NI NI . D NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc17 D NE2 HIS 146 D HIS 149 1_555 J NI NI . D NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? # _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 6JFD _atom_sites.fract_transf_matrix[1][1] 0.022558 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008166 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006833 _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] 0.016285 _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 2 NI B 1 201 3 NI NI . G 2 NI B 1 202 6 NI NI . H 2 NI C 1 201 1 NI NI . I 3 K1U C 1 202 1 K1U K1U . J 2 NI D 1 201 4 NI NI . K 2 NI D 1 202 5 NI NI . L 4 HOH A 1 301 22 HOH HOH . L 4 HOH A 2 302 8 HOH HOH . L 4 HOH A 3 303 14 HOH HOH . L 4 HOH A 4 304 15 HOH HOH . M 4 HOH B 1 301 23 HOH HOH . M 4 HOH B 2 302 4 HOH HOH . M 4 HOH B 3 303 18 HOH HOH . M 4 HOH B 4 304 9 HOH HOH . M 4 HOH B 5 305 5 HOH HOH . M 4 HOH B 6 306 19 HOH HOH . N 4 HOH C 1 301 13 HOH HOH . N 4 HOH C 2 302 11 HOH HOH . N 4 HOH C 3 303 16 HOH HOH . N 4 HOH C 4 304 25 HOH HOH . N 4 HOH C 5 305 21 HOH HOH . O 4 HOH D 1 301 12 HOH HOH . O 4 HOH D 2 302 17 HOH HOH . O 4 HOH D 3 303 7 HOH HOH . O 4 HOH D 4 304 3 HOH HOH . O 4 HOH D 5 305 6 HOH HOH . O 4 HOH D 6 306 20 HOH HOH . O 4 HOH D 7 307 24 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 J _atom_site.label_entity_id 2 _atom_site.Cartn_x -9.769 _atom_site.Cartn_y -7.588 _atom_site.Cartn_z 33.342 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 92.55 _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 D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #