data_5DMV # _model_server_result.job_id 8p3CvXbhyZ8Jzt8CbUUtIA _model_server_result.datetime_utc '2024-11-09 01:54:00' _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 5dmv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":702}' # _entry.id 5DMV # _exptl.entry_id 5DMV _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.2 _cell.angle_gamma 90 _cell.entry_id 5DMV _cell.length_a 35.627 _cell.length_b 63.329 _cell.length_c 56.831 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DMV _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 C N N ? 3 D N N ? 3 E 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 covale ? covale1 B C SER 6 D SER 151 1_555 B N TPO 7 D TPO 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 B C TPO 7 D TPO 152 1_555 B N ILE 8 D ILE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? metalc ? metalc1 A NE2 HIS 102 C HIS 468 1_555 E NI NI . C NI 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc2 A NE2 HIS 123 C HIS 489 1_555 C NI NI . C NI 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc3 A NE2 HIS 172 C HIS 538 1_555 D NI NI . C NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc4 C NI NI . C NI 701 1_555 F O HOH . C HOH 825 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc5 C NI NI . C NI 701 1_555 F O HOH . C HOH 832 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc6 C NI NI . C NI 701 1_555 F O HOH . C HOH 834 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc7 D NI NI . C NI 702 1_555 F O HOH . C HOH 818 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc8 E NI NI . C NI 703 1_555 F O HOH . C HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? # _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 5DMV _atom_sites.fract_transf_matrix[1][1] 0.028069 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003545 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015791 _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] 0.017736 _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 C 1 701 1 NI NI . D 3 NI C 1 702 2 NI NI . E 3 NI C 1 703 3 NI NI . F 4 HOH C 1 801 35 HOH HOH . F 4 HOH C 2 802 15 HOH HOH . F 4 HOH C 3 803 30 HOH HOH . F 4 HOH C 4 804 25 HOH HOH . F 4 HOH C 5 805 4 HOH HOH . F 4 HOH C 6 806 24 HOH HOH . F 4 HOH C 7 807 20 HOH HOH . F 4 HOH C 8 808 22 HOH HOH . F 4 HOH C 9 809 3 HOH HOH . F 4 HOH C 10 810 6 HOH HOH . F 4 HOH C 11 811 2 HOH HOH . F 4 HOH C 12 812 29 HOH HOH . F 4 HOH C 13 813 19 HOH HOH . F 4 HOH C 14 814 10 HOH HOH . F 4 HOH C 15 815 17 HOH HOH . F 4 HOH C 16 816 26 HOH HOH . F 4 HOH C 17 817 36 HOH HOH . F 4 HOH C 18 818 9 HOH HOH . F 4 HOH C 19 819 13 HOH HOH . F 4 HOH C 20 820 38 HOH HOH . F 4 HOH C 21 821 23 HOH HOH . F 4 HOH C 22 822 8 HOH HOH . F 4 HOH C 23 823 18 HOH HOH . F 4 HOH C 24 824 28 HOH HOH . F 4 HOH C 25 825 11 HOH HOH . F 4 HOH C 26 826 34 HOH HOH . F 4 HOH C 27 827 37 HOH HOH . F 4 HOH C 28 828 14 HOH HOH . F 4 HOH C 29 829 27 HOH HOH . F 4 HOH C 30 830 33 HOH HOH . F 4 HOH C 31 831 12 HOH HOH . F 4 HOH C 32 832 31 HOH HOH . F 4 HOH C 33 833 16 HOH HOH . F 4 HOH C 34 834 32 HOH HOH . F 4 HOH C 35 835 7 HOH HOH . F 4 HOH C 36 836 21 HOH HOH . G 4 HOH D 1 201 5 HOH HOH . G 4 HOH D 2 202 1 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 3 _atom_site.Cartn_x 103.147 _atom_site.Cartn_y -75.401 _atom_site.Cartn_z 7.47 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 70.2 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 702 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #