data_5YPB
#
_model_server_result.job_id            Ig5bIyk976lde86pLnb-cw 
_model_server_result.datetime_utc      '2024-11-05 09:30:12' 
_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          5ypb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":101}' 
#
_entry.id    5YPB 
#
_exptl.entry_id    5YPB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              65.409 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'ZINC ION' 
_entity.pdbx_number_of_molecules    8 
_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            5YPB 
_cell.length_a            113.981 
_cell.length_b            113.981 
_cell.length_c            113.981 
_cell.Z_PDB               96 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YPB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        197 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 3' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,M 1 1 
B,G,H,N 2 1 
C,I,J,O 3 1 
D,K,L,P 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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 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 SG CYS 8 A CYS 4 1_555 E ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc2 A SG CYS 11 A CYS 7 1_555 E ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc3 A SG CYS 22 A CYS 18 1_555 F ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc4 A SG CYS 25 A CYS 21 1_555 F ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc5 A SG CYS 31 A CYS 27 1_555 E ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? 
metalc ? metalc6 A SG CYS 34 A CYS 30 1_555 E ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc7 A NE2 HIS 40 A HIS 36 1_555 F ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc8 A ND1 HIS 43 A HIS 39 1_555 F ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc9 B SG CYS 8 B CYS 4 1_555 G ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc10 B SG CYS 11 B CYS 7 1_555 G ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc11 B SG CYS 22 B CYS 18 1_555 H ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc12 B SG CYS 25 B CYS 21 1_555 H ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc13 B SG CYS 31 B CYS 27 1_555 G ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? 
metalc ? metalc14 B SG CYS 34 B CYS 30 1_555 G ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc15 B NE2 HIS 40 B HIS 36 1_555 H ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc16 B ND1 HIS 43 B HIS 39 1_555 H ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc17 C SG CYS 8 C CYS 4 1_555 I ZN ZN . C ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc18 C SG CYS 11 C CYS 7 1_555 I ZN ZN . C ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc19 C SG CYS 22 C CYS 18 1_555 J ZN ZN . C ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc20 C SG CYS 25 C CYS 21 1_555 J ZN ZN . C ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc21 C SG CYS 31 C CYS 27 1_555 I ZN ZN . C ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc22 C SG CYS 34 C CYS 30 1_555 I ZN ZN . C ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc23 C NE2 HIS 40 C HIS 36 1_555 J ZN ZN . C ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc24 C ND1 HIS 43 C HIS 39 1_555 J ZN ZN . C ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? 
metalc ? metalc25 D SG CYS 8 D CYS 4 1_555 K ZN ZN . D ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc26 D SG CYS 11 D CYS 7 1_555 K ZN ZN . D ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc27 D SG CYS 22 D CYS 18 1_555 L ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc28 D SG CYS 25 D CYS 21 1_555 L ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc29 D SG CYS 31 D CYS 27 1_555 K ZN ZN . D ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc30 D SG CYS 34 D CYS 30 1_555 K ZN ZN . D ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc31 D NE2 HIS 40 D HIS 36 1_555 L ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc32 D ND1 HIS 43 D HIS 39 1_555 L ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
#
_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                     5YPB 
_atom_sites.fract_transf_matrix[1][1]    0.008773 
_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]    0.008773 
_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]    0.008773 
_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 ZN A 1 101 1 ZN ZN . 
F 2 ZN A 1 102 2 ZN ZN . 
G 2 ZN B 1 101 3 ZN ZN . 
H 2 ZN B 1 102 4 ZN ZN . 
I 2 ZN C 1 101 5 ZN ZN . 
J 2 ZN C 1 102 6 ZN ZN . 
K 2 ZN D 1 101 7 ZN ZN . 
L 2 ZN D 1 102 8 ZN ZN . 
M 3 HOH A 1 201 6 HOH HOH . 
M 3 HOH A 2 202 1 HOH HOH . 
M 3 HOH A 3 203 20 HOH HOH . 
N 3 HOH B 1 201 16 HOH HOH . 
N 3 HOH B 2 202 7 HOH HOH . 
N 3 HOH B 3 203 5 HOH HOH . 
N 3 HOH B 4 204 14 HOH HOH . 
N 3 HOH B 5 205 11 HOH HOH . 
N 3 HOH B 6 206 13 HOH HOH . 
N 3 HOH B 7 207 2 HOH HOH . 
N 3 HOH B 8 208 17 HOH HOH . 
N 3 HOH B 9 209 22 HOH HOH . 
O 3 HOH C 1 201 8 HOH HOH . 
O 3 HOH C 2 202 10 HOH HOH . 
O 3 HOH C 3 203 9 HOH HOH . 
O 3 HOH C 4 204 3 HOH HOH . 
P 3 HOH D 1 201 18 HOH HOH . 
P 3 HOH D 2 202 4 HOH HOH . 
P 3 HOH D 3 203 12 HOH HOH . 
P 3 HOH D 4 204 19 HOH HOH . 
#
_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         E 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               -18.238 
_atom_site.Cartn_y               -26.965 
_atom_site.Cartn_z               -42.835 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        38.23 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          ZN 
_atom_site.auth_comp_id          ZN 
_atom_site.auth_seq_id           101 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#