data_3BKV # _model_server_result.job_id fbZeCrdAgdzq28Ng3WXblg _model_server_result.datetime_utc '2025-07-06 03:33:31' _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 3bkv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 3BKV # _exptl.entry_id 3BKV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 1 _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 3BKV _cell.length_a 62.322 _cell.length_b 62.322 _cell.length_c 182.643 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BKV _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 NAG NAG C1 O1 . O4 HO4 . 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 2 n B NAG 1 B 1 NAG A 504 NAG 2 n B NAG 2 B 2 NAG A 503 NAG 2 n B NAG 3 B 3 NAG A 502 NAG 2 n B NAG 4 B 4 NAG A 501 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 covale ? covale1 A C ILE 8 A ILE 0 1_555 A N MSE 9 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 A C MSE 9 A MSE 1 1_555 A N LYS 10 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 A C PRO 87 A PRO 79 1_555 A N MSE 88 A MSE 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 A C MSE 88 A MSE 80 1_555 A N PRO 89 A PRO 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale5 A C VAL 101 A VAL 93 1_555 A N MSE 102 A MSE 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 A C MSE 102 A MSE 94 1_555 A N ASN 103 A ASN 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C THR 150 A THR 142 1_555 A N MSE 151 A MSE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C MSE 151 A MSE 143 1_555 A N ILE 152 A ILE 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale9 A C GLY 156 A GLY 148 1_555 A N MSE 157 A MSE 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 A C MSE 157 A MSE 149 1_555 A N LYS 158 A LYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 A C LEU 178 A LEU 170 1_555 A N MSE 179 A MSE 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale12 A C MSE 179 A MSE 171 1_555 A N GLY 180 A GLY 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale13 A C ASN 187 A ASN 179 1_555 A N MSE 188 A MSE 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 A C MSE 188 A MSE 180 1_555 A N ASN 189 A ASN 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 A C LEU 258 A LEU 250 1_555 A N MSE 259 A MSE 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale16 A C MSE 259 A MSE 251 1_555 A N ASP 260 A ASP 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale17 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale18 B O4 NAG . B NAG 2 1_555 B C1 NAG . B NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale19 B O4 NAG . B NAG 3 1_555 B C1 NAG . B NAG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? # _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 3BKV _atom_sites.fract_transf_matrix[1][1] 0.016046 _atom_sites.fract_transf_matrix[1][2] 0.009264 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018528 _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] 0.005475 _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 C 3 NI A 1 601 601 NI NI . D 4 SO4 A 1 602 602 SO4 SO4 . E 5 HOH A 1 603 603 HOH HOH . E 5 HOH A 2 604 604 HOH HOH . E 5 HOH A 3 605 605 HOH HOH . E 5 HOH A 4 606 606 HOH HOH . E 5 HOH A 5 607 607 HOH HOH . E 5 HOH A 6 608 608 HOH HOH . E 5 HOH A 7 609 609 HOH HOH . E 5 HOH A 8 610 610 HOH HOH . E 5 HOH A 9 611 611 HOH HOH . E 5 HOH A 10 612 612 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 C _atom_site.label_entity_id 3 _atom_site.Cartn_x 29.119 _atom_site.Cartn_y -4.984 _atom_site.Cartn_z -6.595 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 48.5 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 601 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #