data_4RA0 # _model_server_result.job_id yDHBnxRyaR3WiDMama2GDg _model_server_result.datetime_utc '2024-11-23 00:11:53' _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 4ra0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":301}' # _entry.id 4RA0 # _exptl.entry_id 4RA0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 6 _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 4RA0 _cell.length_a 112.37 _cell.length_b 112.37 _cell.length_c 361.26 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RA0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 6 J N N ? 6 L N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n E NAG 1 E 1 NAG A 1678 NAG 3 n E NAG 2 E 2 NAG A 1679 NAG 3 n F NAG 1 F 1 NAG B 1678 NAG 3 n F NAG 2 F 2 NAG B 1679 NAG # 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 disulf ? disulf1 A SG CYS 6 A CYS 283 1_555 A SG CYS 293 A CYS 570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf2 A SG CYS 167 A CYS 444 1_555 A SG CYS 193 A CYS 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 366 A CYS 643 1_555 A SG CYS 393 A CYS 670 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf4 B SG CYS 6 B CYS 283 1_555 B SG CYS 293 B CYS 570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 B SG CYS 167 B CYS 444 1_555 B SG CYS 193 B CYS 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf6 B SG CYS 366 B CYS 643 1_555 B SG CYS 393 B CYS 670 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf7 C SG CYS 24 C CYS 49 1_555 C SG CYS 85 C CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf8 C SG CYS 128 C CYS 153 1_555 C SG CYS 173 C CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 D SG CYS 24 D CYS 49 1_555 D SG CYS 85 D CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 D SG CYS 128 D CYS 153 1_555 D SG CYS 173 D CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? covale ? covale1 A ND2 ASN 143 A ASN 420 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 B ND2 ASN 143 B ASN 420 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? metalc ? metalc1 A OD2 ASP 52 A ASP 329 1_555 G CA CA . A CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc2 A OD1 ASP 52 A ASP 329 1_555 G CA CA . A CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc3 A O GLU 54 A GLU 331 1_555 G CA CA . A CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc4 A O ARG 163 A ARG 440 1_555 G CA CA . A CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc5 A OD2 ASP 379 A ASP 656 1_555 G CA CA . A CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc6 B OD2 ASP 52 B ASP 329 1_555 I CA CA . B CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc7 B OD1 ASP 52 B ASP 329 1_555 I CA CA . B CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc8 B O GLU 54 B GLU 331 1_555 I CA CA . B CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc9 B O ARG 163 B ARG 440 1_555 I CA CA . B CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc10 B OD2 ASP 379 B ASP 656 1_555 I CA CA . B CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc11 C ND1 HIS 154 C HIS 179 1_555 J NI NI . C NI 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc12 D NE2 HIS 154 D HIS 179 1_555 L NI NI . D NI 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? # _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 4RA0 _atom_sites.fract_transf_matrix[1][1] 0.008899 _atom_sites.fract_transf_matrix[1][2] 0.005138 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010276 _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] 0.002768 _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 G 4 CA A 1 703 1 CA CA . H 5 CL A 1 704 7 CL CL . I 4 CA B 1 703 2 CA CA . J 6 NI C 1 301 3 NI NI . K 7 SO4 C 1 302 5 SO4 SO4 . L 6 NI D 1 301 4 NI NI . M 7 SO4 D 1 302 6 SO4 SO4 . N 8 HOH A 1 801 1 HOH HOH . N 8 HOH A 2 802 10 HOH HOH . N 8 HOH A 3 803 11 HOH HOH . N 8 HOH A 4 804 14 HOH HOH . N 8 HOH A 5 805 15 HOH HOH . O 8 HOH B 1 801 2 HOH HOH . O 8 HOH B 2 802 3 HOH HOH . O 8 HOH B 3 803 4 HOH HOH . O 8 HOH B 4 804 5 HOH HOH . O 8 HOH B 5 805 12 HOH HOH . P 8 HOH C 1 401 16 HOH HOH . Q 8 HOH D 1 401 7 HOH HOH . Q 8 HOH D 2 402 8 HOH HOH . Q 8 HOH D 3 403 17 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 L _atom_site.label_entity_id 6 _atom_site.Cartn_x 48.33 _atom_site.Cartn_y -15.656 _atom_site.Cartn_z 10.638 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 138.94 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 301 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #