data_6M7U # _model_server_result.job_id 3ybUCezLxsqEKqz5TPQXSQ _model_server_result.datetime_utc '2024-11-01 02:30:57' _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 6m7u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6M7U # _exptl.entry_id 6M7U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 4 _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 90 _cell.entry_id 6M7U _cell.length_a 63.31 _cell.length_b 80.47 _cell.length_c 142.07 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M7U _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H,I,J _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 C O3' DT 2 T DT 3 1_555 C P 02I 3 T 02I 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? covale ? covale2 C O3' 02I 3 T 02I 4 1_555 C P DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc5 A OD1 ASP 184 A ASP 181 1_555 D NI NI . A NI 501 2_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc6 A OD2 ASP 184 A ASP 181 1_555 D NI NI . A NI 501 2_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc7 A NE2 HIS 292 A HIS 289 1_555 D NI NI . A NI 501 3_645 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc8 A NE2 HIS 396 A HIS 393 1_555 D NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc9 A NE2 HIS 400 A HIS 397 1_555 D NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc10 E O1A 1FZ . A 1FZ 502 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc11 E O2B 1FZ . A 1FZ 502 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc12 E O1G 1FZ . A 1FZ 502 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? hydrog WATSON-CRICK hydrog1 B N1 DG 2 P DG 2 1_555 C N3 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 2 P DG 2 1_555 C O2 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 2 P DG 2 1_555 C N4 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 3 P DT 3 1_555 C N1 DA 9 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 3 P DT 3 1_555 C N6 DA 9 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 4 P DG 4 1_555 C N3 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 DG 4 P DG 4 1_555 C O2 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 DG 4 P DG 4 1_555 C N4 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DT 5 P DT 5 1_555 C N1 DA 7 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O4 DT 5 P DT 5 1_555 C N6 DA 7 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DG 6 P DG 6 1_555 C N3 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 DG 6 P DG 6 1_555 C O2 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 6 P DG 6 1_555 C N4 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 7 P DA 7 1_555 C N3 DT 5 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 7 P DA 7 1_555 C O4 DT 5 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 8 P DG 8 1_555 C N3 DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 8 P DG 8 1_555 C O2 DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 8 P DG 8 1_555 C N4 DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 6M7U _atom_sites.fract_transf_matrix[1][1] 0.015795 _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] 0.012427 _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] 0.007039 _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 D 4 NI A 1 501 452 NI NI . E 5 1FZ A 1 502 501 1FZ 1FZ . F 6 MG A 1 503 2 MG MG . G 7 CL A 1 504 1 CL CL . H 8 HOH A 1 601 2 HOH HOH . H 8 HOH A 2 602 15 HOH HOH . H 8 HOH A 3 603 33 HOH HOH . H 8 HOH A 4 604 31 HOH HOH . H 8 HOH A 5 605 3 HOH HOH . H 8 HOH A 6 606 17 HOH HOH . H 8 HOH A 7 607 29 HOH HOH . H 8 HOH A 8 608 30 HOH HOH . H 8 HOH A 9 609 8 HOH HOH . H 8 HOH A 10 610 22 HOH HOH . H 8 HOH A 11 611 28 HOH HOH . H 8 HOH A 12 612 13 HOH HOH . H 8 HOH A 13 613 35 HOH HOH . H 8 HOH A 14 614 36 HOH HOH . H 8 HOH A 15 615 41 HOH HOH . H 8 HOH A 16 616 38 HOH HOH . H 8 HOH A 17 617 14 HOH HOH . H 8 HOH A 18 618 39 HOH HOH . H 8 HOH A 19 619 1 HOH HOH . I 8 HOH P 1 101 26 HOH HOH . J 8 HOH T 1 101 6 HOH HOH . J 8 HOH T 2 102 4 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 D _atom_site.label_entity_id 4 _atom_site.Cartn_x 28.801 _atom_site.Cartn_y 6.963 _atom_site.Cartn_z 56.604 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 56.61 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 501 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #