data_2YPT
#
_model_server_result.job_id            Qiy3o1IePtSXAB4C9GkMYQ 
_model_server_result.datetime_utc      '2025-02-22 17:08:15' 
_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          2ypt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":600}' 
#
_entry.id    2YPT 
#
_exptl.entry_id    2YPT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              65.409 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'ZINC ION' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         76.26 
_cell.angle_beta          79.67 
_cell.angle_gamma         72.3 
_cell.entry_id            2YPT 
_cell.length_a            61.32 
_cell.length_b            95.54 
_cell.length_c            132.03 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YPT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
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 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
C,G,K 1 1 
A,E,I 2 1 
B,F,J 3 1 
D,H,L 4 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 I N N 
? 3 J N N 
? 3 K 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
metalc ? metalc1 A NE2 HIS 335 A HIS 335 1_555 I ZN ZN . A ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc2 A NE2 HIS 339 A HIS 339 1_555 I ZN ZN . A ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc3 A OE2 GLU 415 A GLU 415 1_555 I ZN ZN . A ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc4 I ZN ZN . A ZN 600 1_555 E O SER 2 F SER 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc5 B NE2 HIS 335 B HIS 335 1_555 J ZN ZN . B ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc6 B NE2 HIS 339 B HIS 339 1_555 J ZN ZN . B ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc7 B OE2 GLU 415 B GLU 415 1_555 J ZN ZN . B ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc8 J ZN ZN . B ZN 600 1_555 F O SER 2 G SER 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc9 C NE2 HIS 335 D HIS 335 1_555 K ZN ZN . D ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc10 C NE2 HIS 339 D HIS 339 1_555 K ZN ZN . D ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc11 C OE2 GLU 415 D GLU 415 1_555 K ZN ZN . D ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc12 K ZN ZN . D ZN 600 1_555 G O SER 2 H SER 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc13 D NE2 HIS 335 E HIS 335 1_555 L ZN ZN . E ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc14 D NE2 HIS 339 E HIS 339 1_555 L ZN ZN . E ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc15 D OE2 GLU 415 E GLU 415 1_555 L ZN ZN . E ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc16 L ZN ZN . E ZN 600 1_555 H O SER 2 I SER 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
#
_chem_comp.formula           'Zn 2' 
_chem_comp.formula_weight    65.409 
_chem_comp.id                ZN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'ZINC ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     2YPT 
_atom_sites.fract_transf_matrix[1][1]    0.016308 
_atom_sites.fract_transf_matrix[1][2]    -0.005205 
_atom_sites.fract_transf_matrix[1][3]    -0.001995 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010987 
_atom_sites.fract_transf_matrix[2][3]    -0.002187 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.00785 
_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
I 3 ZN A 1 600 600 ZN ZN . 
J 3 ZN B 1 600 600 ZN ZN . 
K 3 ZN D 1 600 600 ZN ZN . 
L 3 ZN E 1 600 600 ZN ZN . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           ZN 
_atom_site.label_atom_id         ZN 
_atom_site.label_comp_id         ZN 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         L 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               157.924 
_atom_site.Cartn_y               146.678 
_atom_site.Cartn_z               153.749 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        187.12 
_atom_site.pdbx_formal_charge    2 
_atom_site.auth_atom_id          ZN 
_atom_site.auth_comp_id          ZN 
_atom_site.auth_seq_id           600 
_atom_site.auth_asym_id          E 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           1 
#