data_2PED # _model_server_result.job_id ttnJbs7cjngqjte2MUgPQQ _model_server_result.datetime_utc '2024-12-22 12:44:52' _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 2ped # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":902}' # _entry.id 2PED # _exptl.entry_id 2PED _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 200.59 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MERCURY (II) 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 90 _cell.angle_gamma 90 _cell.entry_id 2PED _cell.length_a 95.96 _cell.length_b 95.96 _cell.length_c 150.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PED _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # 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,PQS dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA 1 1 B,E,F,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,HA 2 1 A,C,D,G,H,I,J,K,L,M,N,O,P,Q,R,S,GA 2 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_765 -x+2,-y+1,z+1/2 -1 0 0 0 -1 0 0 0 1 191.92 95.96 75.42 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 H N N ? 5 I N N ? 5 T N N ? 5 U N N ? 5 V N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 4 4 3 BMA BMA C1 O1 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG ? 505 NAG 2 n C NAG 2 C 2 NAG ? 504 NAG 2 n C MAN 3 C 3 MAN ? 503 MAN 3 n D NAG 1 D 1 NAG ? 705 NAG 3 n D NAG 2 D 2 NAG ? 704 NAG 4 n E NAG 1 E 1 NAG ? 605 NAG 4 n E NAG 2 E 2 NAG ? 604 NAG 4 n E BMA 3 E 3 BMA ? 603 BMA 4 n E BMA 4 E 4 BMA ? 602 BMA 3 n F NAG 1 F 1 NAG ? 805 NAG 3 n F NAG 2 F 2 NAG ? 804 NAG # 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 disulf ? disulf1 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 111 B CYS 110 1_555 B SG CYS 188 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A ND2 ASN 3 A ASN 2 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 A ND2 ASN 16 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale4 A NZ LYS 297 A LYS 296 1_555 N C15 RET . A RET 1296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale5 A SG CYS 323 A CYS 322 1_555 O C1 PLM . A PLM 1322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.858 ? covale ? covale6 A SG CYS 324 A CYS 323 1_555 P C1 PLM . A PLM 1323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? covale ? covale7 B C ACE 1 B ACE 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale8 B ND2 ASN 3 B ASN 2 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale9 B ND2 ASN 16 B ASN 15 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale10 B NZ LYS 297 B LYS 296 1_555 Z C15 RET . B RET 1296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale11 B SG CYS 323 B CYS 322 1_555 AA C1 PLM . B PLM 1322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? covale ? covale12 B SG CYS 324 B CYS 323 1_555 BA C1 PLM . B PLM 1323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? covale ? covale13 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale14 C O4 NAG . C NAG 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale15 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale16 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale17 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale18 E O3 BMA . E BMA 3 1_555 E C1 BMA . E BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale19 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? metalc ? metalc1 A NE2 HIS 196 A HIS 195 1_555 M ZN ZN . A ZN 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc2 A OE1 GLU 202 A GLU 201 1_555 J ZN ZN . A ZN 957 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc3 A OE2 GLU 202 A GLU 201 1_555 J ZN ZN . A ZN 957 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc4 A NE2 GLN 280 A GLN 279 1_555 J ZN ZN . A ZN 957 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? metalc ? metalc5 A NZ LYS 312 A LYS 311 1_555 K ZN ZN . A ZN 959 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc6 A N ASP 331 A ASP 330 1_555 K ZN ZN . A ZN 959 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc7 B NE2 HIS 196 B HIS 195 1_555 W ZN ZN . B ZN 956 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc8 B OE2 GLU 202 B GLU 201 1_555 X ZN ZN . B ZN 958 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc9 B O VAL 338 B VAL 337 1_555 V HG HG . B HG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? # _chem_comp.formula 'Hg 2' _chem_comp.formula_weight 200.59 _chem_comp.id HG _chem_comp.mon_nstd_flag . _chem_comp.name 'MERCURY (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2PED _atom_sites.fract_transf_matrix[1][1] 0.010421 _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] 0.010421 _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] 0.00663 _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 G 5 HG A 1 901 901 HG HG . H 5 HG A 1 903 903 HG HG . I 5 HG A 1 905 905 HG HG . J 6 ZN A 1 957 957 ZN ZN . K 6 ZN A 1 959 959 ZN ZN . L 6 ZN A 1 962 962 ZN ZN . M 6 ZN A 1 2011 2011 ZN ZN . N 7 RET A 1 1296 1296 RET RET . O 8 PLM A 1 1322 1322 PLM PLY . P 8 PLM A 1 1323 1323 PLM PLY . Q 8 PLM A 1 1410 1410 PLM PLY . R 9 HTG A 1 1507 1507 HTG HTG . S 9 HTG A 1 1508 1508 HTG HTG . T 5 HG B 1 902 902 HG HG . U 5 HG B 1 904 904 HG HG . V 5 HG B 1 906 906 HG HG . W 6 ZN B 1 956 956 ZN ZN . X 6 ZN B 1 958 958 ZN ZN . Y 6 ZN B 1 963 963 ZN ZN . Z 7 RET B 1 1296 1296 RET RET . AA 8 PLM B 1 1322 1322 PLM PLY . BA 8 PLM B 1 1323 1323 PLM PLY . CA 10 HTO B 1 1401 1401 HTO HTO . DA 8 PLM B 1 1407 1407 PLM PLY . EA 9 HTG B 1 1506 1506 HTG HTG . FA 9 HTG B 1 1509 1509 HTG HTG . GA 11 HOH A 1 964 964 HOH HOH . GA 11 HOH A 2 2000 2000 HOH HOH . GA 11 HOH A 3 2002 2002 HOH HOH . GA 11 HOH A 4 2004 2004 HOH HOH . GA 11 HOH A 5 2007 2007 HOH HOH . GA 11 HOH A 6 2014 2014 HOH HOH . GA 11 HOH A 7 2015 2015 HOH HOH . GA 11 HOH A 8 2017 2017 HOH HOH . GA 11 HOH A 9 2020 2020 HOH HOH . GA 11 HOH A 10 2021 2021 HOH HOH . GA 11 HOH A 11 2024 2024 HOH HOH . GA 11 HOH A 12 2027 2027 HOH HOH . GA 11 HOH A 13 2028 2028 HOH HOH . GA 11 HOH A 14 2030 2030 HOH HOH . GA 11 HOH A 15 2032 2032 HOH HOH . GA 11 HOH A 16 2033 2033 HOH HOH . GA 11 HOH A 17 2035 2035 HOH HOH . GA 11 HOH A 18 2039 2039 HOH HOH . GA 11 HOH A 19 2041 2041 HOH HOH . GA 11 HOH A 20 2042 2042 HOH HOH . GA 11 HOH A 21 2045 2045 HOH HOH . GA 11 HOH A 22 2047 2047 HOH HOH . GA 11 HOH A 23 2048 2048 HOH HOH . GA 11 HOH A 24 2049 2049 HOH HOH . GA 11 HOH A 25 2051 2051 HOH HOH . GA 11 HOH A 26 2052 2052 HOH HOH . GA 11 HOH A 27 2053 2053 HOH HOH . GA 11 HOH A 28 2055 2055 HOH HOH . GA 11 HOH A 29 2057 2057 HOH HOH . GA 11 HOH A 30 2058 2058 HOH HOH . GA 11 HOH A 31 2059 2059 HOH HOH . GA 11 HOH A 32 2061 2061 HOH HOH . GA 11 HOH A 33 2062 2062 HOH HOH . GA 11 HOH A 34 2063 2063 HOH HOH . GA 11 HOH A 35 2064 2064 HOH HOH . GA 11 HOH A 36 2068 2068 HOH HOH . GA 11 HOH A 37 2070 2070 HOH HOH . GA 11 HOH A 38 2072 2072 HOH HOH . GA 11 HOH A 39 2073 2073 HOH HOH . GA 11 HOH A 40 2078 2078 HOH HOH . GA 11 HOH A 41 2079 2079 HOH HOH . GA 11 HOH A 42 2080 2080 HOH HOH . GA 11 HOH A 43 2081 2081 HOH HOH . GA 11 HOH A 44 2085 2085 HOH HOH . GA 11 HOH A 45 2086 2086 HOH HOH . GA 11 HOH A 46 2087 2087 HOH HOH . GA 11 HOH A 47 2088 2088 HOH HOH . GA 11 HOH A 48 2090 2090 HOH HOH . GA 11 HOH A 49 2093 2093 HOH HOH . GA 11 HOH A 50 2096 2096 HOH HOH . GA 11 HOH A 51 2097 2097 HOH HOH . GA 11 HOH A 52 2099 2099 HOH HOH . GA 11 HOH A 53 2100 2100 HOH HOH . GA 11 HOH A 54 2102 2102 HOH HOH . GA 11 HOH A 55 2104 2104 HOH HOH . GA 11 HOH A 56 2105 2105 HOH HOH . GA 11 HOH A 57 2106 2106 HOH HOH . GA 11 HOH A 58 2110 2110 HOH HOH . HA 11 HOH B 1 2005 2005 HOH HOH . HA 11 HOH B 2 2008 2008 HOH HOH . HA 11 HOH B 3 2009 2009 HOH HOH . HA 11 HOH B 4 2012 2012 HOH HOH . HA 11 HOH B 5 2016 2016 HOH HOH . HA 11 HOH B 6 2018 2018 HOH HOH . HA 11 HOH B 7 2019 2019 HOH HOH . HA 11 HOH B 8 2022 2022 HOH HOH . HA 11 HOH B 9 2023 2023 HOH HOH . HA 11 HOH B 10 2025 2025 HOH HOH . HA 11 HOH B 11 2026 2026 HOH HOH . HA 11 HOH B 12 2029 2029 HOH HOH . HA 11 HOH B 13 2031 2031 HOH HOH . HA 11 HOH B 14 2034 2034 HOH HOH . HA 11 HOH B 15 2036 2036 HOH HOH . HA 11 HOH B 16 2037 2037 HOH HOH . HA 11 HOH B 17 2038 2038 HOH HOH . HA 11 HOH B 18 2040 2040 HOH HOH . HA 11 HOH B 19 2043 2043 HOH HOH . HA 11 HOH B 20 2044 2044 HOH HOH . HA 11 HOH B 21 2046 2046 HOH HOH . HA 11 HOH B 22 2050 2050 HOH HOH . HA 11 HOH B 23 2054 2054 HOH HOH . HA 11 HOH B 24 2056 2056 HOH HOH . HA 11 HOH B 25 2060 2060 HOH HOH . HA 11 HOH B 26 2065 2065 HOH HOH . HA 11 HOH B 27 2066 2066 HOH HOH . HA 11 HOH B 28 2067 2067 HOH HOH . HA 11 HOH B 29 2069 2069 HOH HOH . HA 11 HOH B 30 2071 2071 HOH HOH . HA 11 HOH B 31 2074 2074 HOH HOH . HA 11 HOH B 32 2075 2075 HOH HOH . HA 11 HOH B 33 2076 2076 HOH HOH . HA 11 HOH B 34 2077 2077 HOH HOH . HA 11 HOH B 35 2082 2082 HOH HOH . HA 11 HOH B 36 2083 2083 HOH HOH . HA 11 HOH B 37 2084 2084 HOH HOH . HA 11 HOH B 38 2089 2089 HOH HOH . HA 11 HOH B 39 2091 2091 HOH HOH . HA 11 HOH B 40 2092 2092 HOH HOH . HA 11 HOH B 41 2094 2094 HOH HOH . HA 11 HOH B 42 2095 2095 HOH HOH . HA 11 HOH B 43 2098 2098 HOH HOH . HA 11 HOH B 44 2101 2101 HOH HOH . HA 11 HOH B 45 2103 2103 HOH HOH . HA 11 HOH B 46 2107 2107 HOH HOH . HA 11 HOH B 47 2108 2108 HOH HOH . HA 11 HOH B 48 2109 2109 HOH HOH . HA 11 HOH B 49 2111 2111 HOH HOH . HA 11 HOH B 50 2112 2112 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol HG _atom_site.label_atom_id HG _atom_site.label_comp_id HG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id T _atom_site.label_entity_id 5 _atom_site.Cartn_x 87.278 _atom_site.Cartn_y 36.568 _atom_site.Cartn_z 5.727 _atom_site.occupancy 0.77 _atom_site.B_iso_or_equiv 83.6 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id HG _atom_site.auth_comp_id HG _atom_site.auth_seq_id 902 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 1 #