data_2YMK # _model_server_result.job_id cGFy0tkyFOqM2veq5wyobQ _model_server_result.datetime_utc '2024-12-26 21:36:48' _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 2ymk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1049}' # _entry.id 2YMK # _exptl.entry_id 2YMK _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 117.74 _cell.angle_gamma 90 _cell.entry_id 2YMK _cell.length_a 76.354 _cell.length_b 50.724 _cell.length_c 45.738 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YMK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -21.289212 0 40.481281 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I 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 OD2 ASP 9 A ASP 9 2_556 F ZN ZN . B ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc2 A OD2 ASP 28 A ASP 28 1_555 E ZN ZN . A ZN 1050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc3 A NE2 HIS 38 A HIS 38 1_555 D ZN ZN . A ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc4 A OD2 ASP 42 A ASP 42 1_555 D ZN ZN . A ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc5 D ZN ZN . A ZN 1049 1_555 B OE2 GLU 5 B GLU 5 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc6 D ZN ZN . A ZN 1049 2_556 B OD2 ASP 9 B ASP 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.669 ? metalc ? metalc7 D ZN ZN . A ZN 1049 1_555 B OD2 ASP 9 B ASP 9 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.669 ? metalc ? metalc8 E ZN ZN . A ZN 1050 1_555 J O HOH . A HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc9 B OD2 ASP 28 B ASP 28 1_555 G ZN ZN . B ZN 1050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc10 B NE2 HIS 38 B HIS 38 1_555 F ZN ZN . B ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc11 B OD2 ASP 42 B ASP 42 1_555 F ZN ZN . B ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc12 G ZN ZN . B ZN 1050 1_555 K O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc13 G ZN ZN . B ZN 1050 1_555 K O HOH . B HOH 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc14 C OE1 GLU 5 C GLU 5 2_556 H ZN ZN . C ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc15 C OD2 ASP 9 C ASP 9 2_556 H ZN ZN . C ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc16 C OD2 ASP 28 C ASP 28 1_555 I ZN ZN . C ZN 1050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc17 C NE2 HIS 38 C HIS 38 1_555 H ZN ZN . C ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc18 C OD2 ASP 42 C ASP 42 1_555 H ZN ZN . C ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc19 C OD1 ASP 42 C ASP 42 1_555 H ZN ZN . C ZN 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc20 I ZN ZN . C ZN 1050 1_555 L O HOH . C HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? # _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 2YMK _atom_sites.fract_transf_matrix[1][1] 0.013097 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006888 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019715 _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] 0.024703 _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 D 2 ZN A 1 1049 1049 ZN ZN . E 2 ZN A 1 1050 1050 ZN ZN . F 2 ZN B 1 1049 1049 ZN ZN . G 2 ZN B 1 1050 1050 ZN ZN . H 2 ZN C 1 1049 1049 ZN ZN . I 2 ZN C 1 1050 1050 ZN ZN . J 3 HOH A 1 2001 2001 HOH HOH . J 3 HOH A 2 2002 2002 HOH HOH . J 3 HOH A 3 2003 2003 HOH HOH . J 3 HOH A 4 2004 2004 HOH HOH . J 3 HOH A 5 2005 2005 HOH HOH . J 3 HOH A 6 2006 2006 HOH HOH . J 3 HOH A 7 2007 2007 HOH HOH . J 3 HOH A 8 2008 2008 HOH HOH . J 3 HOH A 9 2009 2009 HOH HOH . J 3 HOH A 10 2010 2010 HOH HOH . K 3 HOH B 1 2001 2001 HOH HOH . K 3 HOH B 2 2002 2002 HOH HOH . K 3 HOH B 3 2003 2003 HOH HOH . K 3 HOH B 4 2004 2004 HOH HOH . K 3 HOH B 5 2005 2005 HOH HOH . K 3 HOH B 6 2006 2006 HOH HOH . K 3 HOH B 7 2007 2007 HOH HOH . K 3 HOH B 8 2008 2008 HOH HOH . K 3 HOH B 9 2009 2009 HOH HOH . L 3 HOH C 1 2001 2001 HOH HOH . L 3 HOH C 2 2002 2002 HOH HOH . L 3 HOH C 3 2003 2003 HOH HOH . L 3 HOH C 4 2004 2004 HOH HOH . L 3 HOH C 5 2005 2005 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 F _atom_site.label_entity_id 2 _atom_site.Cartn_x 14.235 _atom_site.Cartn_y 28.324 _atom_site.Cartn_z 16.664 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 70.26 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id ZN _atom_site.auth_comp_id ZN _atom_site.auth_seq_id 1049 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #