data_5VB0 # _model_server_result.job_id 34J8fPknmJqlyX1gaV-zeA _model_server_result.datetime_utc '2025-07-28 18:21:41' _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 5vb0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":203}' # _entry.id 5VB0 # _exptl.entry_id 5VB0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _entity.src_method man _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 90 _cell.angle_gamma 90 _cell.entry_id 5VB0 _cell.length_a 87.608 _cell.length_b 87.608 _cell.length_c 357.038 _cell.Z_PDB 64 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VB0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 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 PISA tetrameric 4 software_defined_assembly 5 PISA tetrameric 4 software_defined_assembly 6 # 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 1 1 C,D,M,N,O,P 2 1 E,F,Q,R,S 3 1 G,H,T,U,V 4 1 A,B,C,D,I,J,K,L,M,N,O,P 5 1 E,F,G,H,Q,R,S,T,U,V 6 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 ? 3 J N N ? 3 K N N ? 3 N N N ? 3 O N N ? 3 S N N ? 3 V 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 7 A HIS 7 1_555 L MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc2 A NE2 HIS 67 A HIS 67 1_555 I MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc3 A OE1 GLU 113 A GLU 113 1_555 I MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc4 A OE1 GLU 128 A GLU 128 1_555 K NI NI . A NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc5 A NE2 HIS 139 A HIS 139 1_555 J NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc6 A NE2 HIS 141 A HIS 141 1_555 J NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc7 A NE2 HIS 142 A HIS 142 1_555 K NI NI . A NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc8 I MN MN . A MN 201 1_555 B NE2 HIS 7 B HIS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc9 J NI NI . A NI 202 1_555 F NE2 HIS 139 F HIS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc10 J NI NI . A NI 202 1_555 F NE2 HIS 141 F HIS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc11 B NE2 HIS 67 B HIS 67 1_555 L MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc12 B OE1 GLU 113 B GLU 113 1_555 L MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc13 C NE2 HIS 7 C HIS 7 1_555 P MN MN . D MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc14 C NE2 HIS 67 C HIS 67 1_555 M MN MN . C MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc15 C OE1 GLU 113 C GLU 113 1_555 M MN MN . C MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc16 C OE1 GLU 128 C GLU 128 1_555 O NI NI . C NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc17 C NE2 HIS 139 C HIS 139 1_555 N NI NI . C NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc18 C NE2 HIS 141 C HIS 141 1_555 N NI NI . C NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc19 C NE2 HIS 142 C HIS 142 1_555 O NI NI . C NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc20 M MN MN . C MN 201 1_555 D NE2 HIS 7 D HIS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc21 N NI NI . C NI 202 1_555 H NE2 HIS 139 H HIS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc22 N NI NI . C NI 202 1_555 H NE2 HIS 141 H HIS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc23 D NE2 HIS 67 D HIS 67 1_555 P MN MN . D MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc24 D OE1 GLU 113 D GLU 113 1_555 P MN MN . D MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc25 E NE2 HIS 7 E HIS 7 1_555 R MN MN . F MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc26 E NE2 HIS 67 E HIS 67 1_555 Q MN MN . E MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc27 E OE1 GLU 113 E GLU 113 1_555 Q MN MN . E MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc28 Q MN MN . E MN 201 1_555 F NE2 HIS 7 F HIS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc29 F NE2 HIS 67 F HIS 67 1_555 R MN MN . F MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc30 F OE1 GLU 113 F GLU 113 1_555 R MN MN . F MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc31 F OE1 GLU 128 F GLU 128 1_555 S NI NI . F NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc32 F NE2 HIS 142 F HIS 142 1_555 S NI NI . F NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc33 G NE2 HIS 7 G HIS 7 1_555 U MN MN . H MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc34 G NE2 HIS 67 G HIS 67 1_555 T MN MN . G MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc35 G OE1 GLU 113 G GLU 113 1_555 T MN MN . G MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc36 T MN MN . G MN 201 1_555 H NE2 HIS 7 H HIS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc37 H NE2 HIS 67 H HIS 67 1_555 U MN MN . H MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc38 H OE1 GLU 113 H GLU 113 1_555 U MN MN . H MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc39 H OE1 GLU 128 H GLU 128 1_555 V NI NI . H NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc40 H NE2 HIS 142 H HIS 142 1_555 V NI NI . H NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? # _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 5VB0 _atom_sites.fract_transf_matrix[1][1] 0.011414 _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] 0.011414 _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] 0.002801 _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 MN A 1 201 1 MN MN . J 3 NI A 1 202 1 NI NI . K 3 NI A 1 203 2 NI NI . L 2 MN B 1 201 2 MN MN . M 2 MN C 1 201 3 MN MN . N 3 NI C 1 202 3 NI NI . O 3 NI C 1 203 4 NI NI . P 2 MN D 1 201 4 MN MN . Q 2 MN E 1 201 5 MN MN . R 2 MN F 1 201 6 MN MN . S 3 NI F 1 202 5 NI NI . T 2 MN G 1 201 7 MN MN . U 2 MN H 1 201 8 MN MN . V 3 NI H 1 202 6 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 O _atom_site.label_entity_id 3 _atom_site.Cartn_x 73.51 _atom_site.Cartn_y 33.686 _atom_site.Cartn_z 395.792 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 87.79 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 203 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #