data_1YKF # _model_server_result.job_id 19xYuW3qYp1PaUbL7RTbBA _model_server_result.datetime_utc '2024-11-15 12:01:08' _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 1ykf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":354}' # _entry.id 1YKF # _exptl.entry_id 1YKF _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 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 1YKF _cell.length_a 80.614 _cell.length_b 80.614 _cell.length_c 400.335 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 G N N ? 2 I N N ? 2 K 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 37 A CYS 37 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc2 A NE2 HIS 59 A HIS 59 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc3 A OD2 ASP 150 A ASP 150 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc4 B SG CYS 37 B CYS 37 1_555 G ZN ZN . B ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? metalc ? metalc5 B NE2 HIS 59 B HIS 59 1_555 G ZN ZN . B ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc6 B OD2 ASP 150 B ASP 150 1_555 G ZN ZN . B ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc7 C SG CYS 37 C CYS 37 1_555 I ZN ZN . C ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? metalc ? metalc8 C NE2 HIS 59 C HIS 59 1_555 I ZN ZN . C ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc9 C OD2 ASP 150 C ASP 150 1_555 I ZN ZN . C ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc10 D SG CYS 37 D CYS 37 1_555 K ZN ZN . D ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc11 D NE2 HIS 59 D HIS 59 1_555 K ZN ZN . D ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc12 D OD2 ASP 150 D ASP 150 1_555 K ZN ZN . D ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? # _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 1YKF _atom_sites.fract_transf_matrix[1][1] 0.012405 _atom_sites.fract_transf_matrix[1][2] 0.007162 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014324 _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] 0.002498 _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 1 354 354 ZN ZN . F 3 NAP A 1 353 353 NAP NAP . G 2 ZN B 1 354 354 ZN ZN . H 3 NAP B 1 353 353 NAP NAP . I 2 ZN C 1 354 354 ZN ZN . J 3 NAP C 1 353 353 NAP NAP . K 2 ZN D 1 354 354 ZN ZN . L 3 NAP D 1 353 353 NAP NAP . M 4 HOH A 1 355 1 HOH HOH . M 4 HOH A 2 356 2 HOH HOH . M 4 HOH A 3 357 3 HOH HOH . M 4 HOH A 4 358 4 HOH HOH . M 4 HOH A 5 359 5 HOH HOH . M 4 HOH A 6 360 6 HOH HOH . M 4 HOH A 7 361 7 HOH HOH . M 4 HOH A 8 362 8 HOH HOH . M 4 HOH A 9 363 9 HOH HOH . M 4 HOH A 10 364 13 HOH HOH . N 4 HOH B 1 355 10 HOH HOH . N 4 HOH B 2 356 11 HOH HOH . N 4 HOH B 3 357 12 HOH HOH . N 4 HOH B 4 358 14 HOH HOH . N 4 HOH B 5 359 15 HOH HOH . N 4 HOH B 6 360 16 HOH HOH . N 4 HOH B 7 361 17 HOH HOH . N 4 HOH B 8 362 18 HOH HOH . N 4 HOH B 9 363 19 HOH HOH . N 4 HOH B 10 364 20 HOH HOH . O 4 HOH C 1 355 21 HOH HOH . O 4 HOH C 2 356 22 HOH HOH . O 4 HOH C 3 357 23 HOH HOH . O 4 HOH C 4 358 25 HOH HOH . O 4 HOH C 5 359 26 HOH HOH . O 4 HOH C 6 360 27 HOH HOH . O 4 HOH C 7 361 28 HOH HOH . O 4 HOH C 8 362 29 HOH HOH . O 4 HOH C 9 363 30 HOH HOH . O 4 HOH C 10 364 31 HOH HOH . O 4 HOH C 11 365 32 HOH HOH . P 4 HOH D 1 355 24 HOH HOH . P 4 HOH D 2 356 33 HOH HOH . P 4 HOH D 3 357 34 HOH HOH . P 4 HOH D 4 358 35 HOH HOH . P 4 HOH D 5 359 36 HOH HOH . P 4 HOH D 6 360 37 HOH HOH . P 4 HOH D 7 361 38 HOH HOH . P 4 HOH D 8 362 39 HOH HOH . P 4 HOH D 9 363 40 HOH HOH . P 4 HOH D 10 364 41 HOH HOH . P 4 HOH D 11 365 42 HOH HOH . P 4 HOH D 12 366 43 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 K _atom_site.label_entity_id 2 _atom_site.Cartn_x 14.428 _atom_site.Cartn_y 6.84 _atom_site.Cartn_z -6.89 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 92.01 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id ZN _atom_site.auth_comp_id ZN _atom_site.auth_seq_id 354 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #