data_5DMV
#
_model_server_result.job_id            j9RuiIcSDdl-uY7ymiJQRA 
_model_server_result.datetime_utc      '2024-11-09 01:54:01' 
_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":"E","auth_seq_id":703}' 
#
_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         E 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               114.416 
_atom_site.Cartn_y               -76.738 
_atom_site.Cartn_z               44.659 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        100.35 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           703 
_atom_site.auth_asym_id          C 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#