data_3RDH
#
_model_server_result.job_id            x2w3UWBpHbIzD-ro6nl0ZQ 
_model_server_result.datetime_utc      '2025-03-04 23:03:44' 
_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          3rdh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":247}' 
#
_entry.id    3RDH 
#
_exptl.entry_id    3RDH 
_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    4 
_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            3RDH 
_cell.length_a            94.745 
_cell.length_b            94.745 
_cell.length_c            237.862 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RDH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
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 tetrameric 4 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,K,L,M,P 1 1 
B,C,G,H,I,J,N,O 2 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 3 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 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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 A NZ LYS 123 A LYS 120 1_555 E N3 3RD . A 3RD 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.204 doub 
covale ? covale2 B NZ LYS 123 B LYS 120 1_555 G N3 3RD . B 3RD 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.2 doub 
covale ? covale3 C NZ LYS 123 C LYS 120 1_555 I N3 3RD . C 3RD 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.211 doub 
covale ? covale4 D NZ LYS 123 D LYS 120 1_555 K N3 3RD . D 3RD 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.207 doub 
metalc ? metalc1 A N GLY 1 A GLY -2 1_555 F NI NI . A NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? 
metalc ? metalc2 A N SER 2 A SER -1 1_555 F NI NI . A NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? 
metalc ? metalc3 A ND1 HIS 3 A HIS 0 1_555 F NI NI . A NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc4 A N HIS 3 A HIS 0 1_555 F NI NI . A NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc5 B N GLY 1 B GLY -2 1_555 H NI NI . B NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? 
metalc ? metalc6 B N HIS 3 B HIS 0 1_555 H NI NI . B NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc7 B ND1 HIS 3 B HIS 0 1_555 H NI NI . B NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc8 C N GLY 1 C GLY -2 1_555 J NI NI . C NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.751 ? 
metalc ? metalc9 C N SER 2 C SER -1 1_555 J NI NI . C NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? 
metalc ? metalc10 C ND1 HIS 3 C HIS 0 1_555 J NI NI . C NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.859 ? 
metalc ? metalc11 C N HIS 3 C HIS 0 1_555 J NI NI . C NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc12 D N GLY 1 D GLY -2 1_555 L NI NI . D NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
metalc ? metalc13 D N SER 2 D SER -1 1_555 L NI NI . D NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? 
metalc ? metalc14 D ND1 HIS 3 D HIS 0 1_555 L NI NI . D NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? 
metalc ? metalc15 D N HIS 3 D HIS 0 1_555 L NI NI . D NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? 
#
_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                     3RDH 
_atom_sites.fract_transf_matrix[1][1]    0.010555 
_atom_sites.fract_transf_matrix[1][2]    0.006094 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012187 
_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]    0.004204 
_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
E 2 3RD A 1 246 231 3RD 3RD . 
F 3 NI A 1 247 1 NI NI . 
G 2 3RD B 1 246 231 3RD 3RD . 
H 3 NI B 1 247 2 NI NI . 
I 2 3RD C 1 246 231 3RD 3RD . 
J 3 NI C 1 247 3 NI NI . 
K 2 3RD D 1 246 231 3RD 3RD . 
L 3 NI D 1 247 4 NI NI . 
M 4 HOH A 1 248 4 HOH TIP . 
M 4 HOH A 2 249 5 HOH TIP . 
M 4 HOH A 3 250 6 HOH TIP . 
M 4 HOH A 4 251 11 HOH TIP . 
M 4 HOH A 5 252 12 HOH TIP . 
M 4 HOH A 6 253 13 HOH TIP . 
M 4 HOH A 7 254 14 HOH TIP . 
M 4 HOH A 8 255 23 HOH TIP . 
M 4 HOH A 9 256 24 HOH TIP . 
M 4 HOH A 10 257 25 HOH TIP . 
M 4 HOH A 11 258 26 HOH TIP . 
M 4 HOH A 12 259 51 HOH TIP . 
M 4 HOH A 13 260 53 HOH TIP . 
M 4 HOH A 14 261 54 HOH TIP . 
M 4 HOH A 15 262 62 HOH TIP . 
M 4 HOH A 16 263 63 HOH TIP . 
M 4 HOH A 17 264 64 HOH TIP . 
M 4 HOH A 18 265 77 HOH TIP . 
M 4 HOH A 19 266 78 HOH TIP . 
M 4 HOH A 20 267 79 HOH TIP . 
M 4 HOH A 21 268 80 HOH TIP . 
N 4 HOH B 1 248 3 HOH TIP . 
N 4 HOH B 2 249 10 HOH TIP . 
N 4 HOH B 3 250 21 HOH TIP . 
N 4 HOH B 4 251 22 HOH TIP . 
N 4 HOH B 5 252 33 HOH TIP . 
N 4 HOH B 6 253 34 HOH TIP . 
N 4 HOH B 7 254 35 HOH TIP . 
N 4 HOH B 8 255 38 HOH TIP . 
N 4 HOH B 9 256 39 HOH TIP . 
N 4 HOH B 10 257 40 HOH TIP . 
N 4 HOH B 11 258 41 HOH TIP . 
N 4 HOH B 12 259 42 HOH TIP . 
N 4 HOH B 13 260 43 HOH TIP . 
N 4 HOH B 14 261 44 HOH TIP . 
N 4 HOH B 15 262 45 HOH TIP . 
N 4 HOH B 16 263 48 HOH TIP . 
N 4 HOH B 17 264 49 HOH TIP . 
N 4 HOH B 18 265 50 HOH TIP . 
N 4 HOH B 19 266 66 HOH TIP . 
N 4 HOH B 20 267 68 HOH TIP . 
N 4 HOH B 21 268 70 HOH TIP . 
N 4 HOH B 22 269 71 HOH TIP . 
N 4 HOH B 23 270 74 HOH TIP . 
N 4 HOH B 24 271 76 HOH TIP . 
O 4 HOH C 1 248 7 HOH TIP . 
O 4 HOH C 2 249 8 HOH TIP . 
O 4 HOH C 3 250 9 HOH TIP . 
O 4 HOH C 4 251 27 HOH TIP . 
O 4 HOH C 5 252 28 HOH TIP . 
O 4 HOH C 6 253 29 HOH TIP . 
O 4 HOH C 7 254 30 HOH TIP . 
O 4 HOH C 8 255 31 HOH TIP . 
O 4 HOH C 9 256 32 HOH TIP . 
O 4 HOH C 10 257 52 HOH TIP . 
O 4 HOH C 11 258 61 HOH TIP . 
O 4 HOH C 12 259 65 HOH TIP . 
O 4 HOH C 13 260 67 HOH TIP . 
O 4 HOH C 14 261 69 HOH TIP . 
O 4 HOH C 15 262 72 HOH TIP . 
O 4 HOH C 16 263 73 HOH TIP . 
O 4 HOH C 17 264 81 HOH TIP . 
O 4 HOH C 18 265 82 HOH TIP . 
O 4 HOH C 19 266 83 HOH TIP . 
O 4 HOH C 20 267 84 HOH TIP . 
O 4 HOH C 21 268 85 HOH TIP . 
P 4 HOH D 1 248 1 HOH TIP . 
P 4 HOH D 2 249 2 HOH TIP . 
P 4 HOH D 3 250 15 HOH TIP . 
P 4 HOH D 4 251 16 HOH TIP . 
P 4 HOH D 5 252 17 HOH TIP . 
P 4 HOH D 6 253 18 HOH TIP . 
P 4 HOH D 7 254 19 HOH TIP . 
P 4 HOH D 8 255 20 HOH TIP . 
P 4 HOH D 9 256 36 HOH TIP . 
P 4 HOH D 10 257 37 HOH TIP . 
P 4 HOH D 11 258 46 HOH TIP . 
P 4 HOH D 12 259 47 HOH TIP . 
P 4 HOH D 13 260 55 HOH TIP . 
P 4 HOH D 14 261 56 HOH TIP . 
P 4 HOH D 15 262 57 HOH TIP . 
P 4 HOH D 16 263 58 HOH TIP . 
P 4 HOH D 17 264 59 HOH TIP . 
P 4 HOH D 18 265 60 HOH TIP . 
P 4 HOH D 19 266 75 HOH TIP . 
P 4 HOH D 20 267 86 HOH TIP . 
#
_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         J 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               -84.583 
_atom_site.Cartn_y               43.557 
_atom_site.Cartn_z               -1.453 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        42.27 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           247 
_atom_site.auth_asym_id          C 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#