data_5YIR
#
_model_server_result.job_id            i6CvZrchXYwcKfPYFA8_Vg 
_model_server_result.datetime_utc      '2024-12-26 11:15:41' 
_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          5yir 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":202}' 
#
_entry.id    5YIR 
#
_exptl.entry_id    5YIR 
_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    10 
_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            5YIR 
_cell.length_a            84.637 
_cell.length_b            84.637 
_cell.length_c            89.344 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YIR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
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 dimeric 2 author_and_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,G,H,I,Q,T 1 1 
B,E,J,K,L,M,R,U 2 1 
C,F,N,O,P,S,V 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 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 P 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
metalc ? metalc1 A NE2 HIS 69 D HIS 69 1_555 N NI NI . B NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc2 A OE1 GLU 97 D GLU 97 1_555 H NI NI . D NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc3 A NE2 HIS 98 D HIS 98 1_555 H NI NI . D NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? 
metalc ? metalc4 A NE2 HIS 99 D HIS 99 1_555 G NI NI . D NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc5 A OE1 GLU 112 D GLU 112 1_555 G NI NI . D NI 201 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc6 G NI NI . D NI 201 1_555 Q O HOH . D HOH 303 2_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc7 G NI NI . D NI 201 1_555 Q O HOH . D HOH 304 2_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc8 I NI NI . D NI 203 1_555 T O HOH . C HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc9 I NI NI . D NI 203 1_555 E OE2 GLU 11 G GLU 1995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc10 I NI NI . D NI 203 1_555 U O HOH . G HOH 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc11 Q O HOH . D HOH 307 1_555 N NI NI . B NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc12 B NE2 HIS 9 A HIS 9 1_555 L NI NI . A NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc13 B NE2 HIS 69 A HIS 69 1_555 K NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc14 B NE2 HIS 98 A HIS 98 1_555 M NI NI . A NI 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc15 B NE2 HIS 99 A HIS 99 1_555 J NI NI . A NI 201 2_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc16 B OE1 GLU 112 A GLU 112 1_555 J NI NI . A NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc17 B OE2 GLU 112 A GLU 112 1_555 J NI NI . A NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc18 J NI NI . A NI 201 1_555 R O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc19 J NI NI . A NI 201 1_555 R O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc20 K NI NI . A NI 202 1_555 R O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc21 K NI NI . A NI 202 1_555 C NE2 HIS 69 B HIS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc22 K NI NI . A NI 202 1_555 S O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc23 L NI NI . A NI 203 1_555 R O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc24 L NI NI . A NI 203 1_555 E OE1 GLU 3 G GLU 1987 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc25 L NI NI . A NI 203 1_555 U O HOH . G HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc26 C NE2 HIS 9 B HIS 9 1_555 N NI NI . B NI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc27 C OE1 GLU 97 B GLU 97 1_555 P NI NI . B NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc28 C NE2 HIS 98 B HIS 98 1_555 P NI NI . B NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? 
metalc ? metalc29 C NE2 HIS 99 B HIS 99 1_555 O NI NI . B NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc30 C OE2 GLU 112 B GLU 112 1_555 O NI NI . B NI 202 3_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc31 N NI NI . B NI 201 1_555 V O HOH . H HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc32 O NI NI . B NI 202 1_555 S O HOH . B HOH 303 2_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc33 O NI NI . B NI 202 1_555 S O HOH . B HOH 304 2_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
#
_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                     5YIR 
_atom_sites.fract_transf_matrix[1][1]    0.011815 
_atom_sites.fract_transf_matrix[1][2]    0.006821 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013643 
_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]    0.011193 
_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
G 3 NI D 1 201 4 NI NI . 
H 3 NI D 1 202 10 NI NI . 
I 3 NI D 1 203 13 NI NI . 
J 3 NI A 1 201 1 NI NI . 
K 3 NI A 1 202 3 NI NI . 
L 3 NI A 1 203 6 NI NI . 
M 3 NI A 1 204 12 NI NI . 
N 3 NI B 1 201 2 NI NI . 
O 3 NI B 1 202 5 NI NI . 
P 3 NI B 1 203 9 NI NI . 
Q 4 HOH D 1 301 22 HOH HOH . 
Q 4 HOH D 2 302 16 HOH HOH . 
Q 4 HOH D 3 303 18 HOH HOH . 
Q 4 HOH D 4 304 19 HOH HOH . 
Q 4 HOH D 5 305 4 HOH HOH . 
Q 4 HOH D 6 306 14 HOH HOH . 
Q 4 HOH D 7 307 12 HOH HOH . 
R 4 HOH A 1 301 9 HOH HOH . 
R 4 HOH A 2 302 2 HOH HOH . 
R 4 HOH A 3 303 10 HOH HOH . 
R 4 HOH A 4 304 8 HOH HOH . 
R 4 HOH A 5 305 20 HOH HOH . 
S 4 HOH B 1 301 7 HOH HOH . 
S 4 HOH B 2 302 1 HOH HOH . 
S 4 HOH B 3 303 6 HOH HOH . 
S 4 HOH B 4 304 5 HOH HOH . 
T 4 HOH C 1 2101 24 HOH HOH . 
U 4 HOH G 1 2101 21 HOH HOH . 
U 4 HOH G 2 2102 25 HOH HOH . 
U 4 HOH G 3 2103 23 HOH HOH . 
V 4 HOH H 1 2101 11 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         H 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               42.891 
_atom_site.Cartn_y               -29.592 
_atom_site.Cartn_z               -11.687 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        106.19 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           202 
_atom_site.auth_asym_id          D 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           248 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#