data_2Y3Y
#
_model_server_result.job_id            CwhLsV4RqnV5FpLC21_whQ 
_model_server_result.datetime_utc      '2024-10-18 18:26:17' 
_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          2y3y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":1143}' 
#
_entry.id    2Y3Y 
#
_exptl.entry_id    2Y3Y 
_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         90 
_cell.entry_id            2Y3Y 
_cell.length_a            72.97 
_cell.length_b            72.97 
_cell.length_c            116.73 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Y3Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,F,G,H,I,J,K,L,M,N,O,P,Q,R 1 1 
E,S 2 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 G N N 
? 3 I N N 
? 3 N 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 31 A HIS 88 1_555 G NI NI . B NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc2 A NE2 HIS 42 A HIS 99 1_555 F NI NI . A NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc3 A ND1 HIS 44 A HIS 101 1_555 F NI NI . A NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc4 A SG CYS 50 A CYS 107 1_555 F NI NI . A NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc5 F NI NI . A NI 1143 1_555 B NE2 HIS 31 B HIS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? 
metalc ? metalc6 B NE2 HIS 42 B HIS 99 1_555 G NI NI . B NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc7 B ND1 HIS 44 B HIS 101 1_555 G NI NI . B NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc8 B SG CYS 50 B CYS 107 1_555 G NI NI . B NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc9 C NE2 HIS 31 C HIS 88 1_555 N NI NI . D NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? 
metalc ? metalc10 C NE2 HIS 42 C HIS 99 1_555 I NI NI . C NI 1142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc11 C ND1 HIS 44 C HIS 101 1_555 I NI NI . C NI 1142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? 
metalc ? metalc12 C SG CYS 50 C CYS 107 1_555 I NI NI . C NI 1142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc13 I NI NI . C NI 1142 1_555 D NE2 HIS 31 D HIS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc14 D NE2 HIS 42 D HIS 99 1_555 N NI NI . D NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? 
metalc ? metalc15 D ND1 HIS 44 D HIS 101 1_555 N NI NI . D NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc16 D SG CYS 50 D CYS 107 1_555 N NI NI . D NI 1143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
#
_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                     2Y3Y 
_atom_sites.fract_transf_matrix[1][1]    0.013704 
_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]    0.013704 
_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]    0.008567 
_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
F 3 NI A 1 1143 1143 NI NI . 
G 3 NI B 1 1143 1143 NI NI . 
H 4 EPE B 1 1144 1144 EPE EPE . 
I 3 NI C 1 1142 1142 NI NI . 
J 4 EPE C 1 1143 1143 EPE EPE . 
K 5 PEG C 1 1144 1144 PEG PEG . 
L 5 PEG C 1 1145 1145 PEG PEG . 
M 5 PEG C 1 1146 1146 PEG PEG . 
N 3 NI D 1 1143 1143 NI NI . 
O 6 HOH A 1 2001 2001 HOH HOH . 
O 6 HOH A 2 2002 2002 HOH HOH . 
O 6 HOH A 3 2003 2003 HOH HOH . 
O 6 HOH A 4 2004 2004 HOH HOH . 
O 6 HOH A 5 2005 2005 HOH HOH . 
O 6 HOH A 6 2006 2006 HOH HOH . 
O 6 HOH A 7 2007 2007 HOH HOH . 
O 6 HOH A 8 2008 2008 HOH HOH . 
O 6 HOH A 9 2009 2009 HOH HOH . 
O 6 HOH A 10 2010 2010 HOH HOH . 
O 6 HOH A 11 2011 2011 HOH HOH . 
O 6 HOH A 12 2012 2012 HOH HOH . 
O 6 HOH A 13 2013 2013 HOH HOH . 
O 6 HOH A 14 2014 2014 HOH HOH . 
O 6 HOH A 15 2015 2015 HOH HOH . 
O 6 HOH A 16 2016 2016 HOH HOH . 
O 6 HOH A 17 2017 2017 HOH HOH . 
O 6 HOH A 18 2018 2018 HOH HOH . 
P 6 HOH B 1 2001 2001 HOH HOH . 
P 6 HOH B 2 2002 2002 HOH HOH . 
P 6 HOH B 3 2003 2003 HOH HOH . 
P 6 HOH B 4 2004 2004 HOH HOH . 
P 6 HOH B 5 2005 2005 HOH HOH . 
P 6 HOH B 6 2006 2006 HOH HOH . 
P 6 HOH B 7 2007 2007 HOH HOH . 
P 6 HOH B 8 2008 2008 HOH HOH . 
P 6 HOH B 9 2009 2009 HOH HOH . 
P 6 HOH B 10 2010 2010 HOH HOH . 
P 6 HOH B 11 2011 2011 HOH HOH . 
P 6 HOH B 12 2012 2012 HOH HOH . 
P 6 HOH B 13 2013 2013 HOH HOH . 
P 6 HOH B 14 2014 2014 HOH HOH . 
P 6 HOH B 15 2015 2015 HOH HOH . 
P 6 HOH B 16 2016 2016 HOH HOH . 
P 6 HOH B 17 2017 2017 HOH HOH . 
Q 6 HOH C 1 2001 2001 HOH HOH . 
Q 6 HOH C 2 2002 2002 HOH HOH . 
Q 6 HOH C 3 2003 2003 HOH HOH . 
Q 6 HOH C 4 2004 2004 HOH HOH . 
Q 6 HOH C 5 2005 2005 HOH HOH . 
Q 6 HOH C 6 2006 2006 HOH HOH . 
Q 6 HOH C 7 2007 2007 HOH HOH . 
Q 6 HOH C 8 2008 2008 HOH HOH . 
Q 6 HOH C 9 2009 2009 HOH HOH . 
Q 6 HOH C 10 2010 2010 HOH HOH . 
Q 6 HOH C 11 2011 2011 HOH HOH . 
Q 6 HOH C 12 2012 2012 HOH HOH . 
Q 6 HOH C 13 2013 2013 HOH HOH . 
Q 6 HOH C 14 2014 2014 HOH HOH . 
Q 6 HOH C 15 2015 2015 HOH HOH . 
Q 6 HOH C 16 2016 2016 HOH HOH . 
Q 6 HOH C 17 2017 2017 HOH HOH . 
R 6 HOH D 1 2001 2001 HOH HOH . 
R 6 HOH D 2 2002 2002 HOH HOH . 
R 6 HOH D 3 2003 2003 HOH HOH . 
R 6 HOH D 4 2004 2004 HOH HOH . 
R 6 HOH D 5 2005 2005 HOH HOH . 
R 6 HOH D 6 2006 2006 HOH HOH . 
R 6 HOH D 7 2007 2007 HOH HOH . 
R 6 HOH D 8 2008 2008 HOH HOH . 
R 6 HOH D 9 2009 2009 HOH HOH . 
R 6 HOH D 10 2010 2010 HOH HOH . 
R 6 HOH D 11 2011 2011 HOH HOH . 
R 6 HOH D 12 2012 2012 HOH HOH . 
R 6 HOH D 13 2013 2013 HOH HOH . 
S 6 HOH Q 1 2001 2001 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         N 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               18.317 
_atom_site.Cartn_y               19.352 
_atom_site.Cartn_z               23.547 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        31.25 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           1143 
_atom_site.auth_asym_id          D 
_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    19 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           1 
#