1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 McElroy, C.A. Amero, C.D. Byerly, D.W. Foster, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C19 H35 N3 O5 385.498 ACTINONIN 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer To be Published 0353 Solution Structure of Peptide Deformylase complexed with Actinonin US Biochemistry BICHAW 0033 0006-2960 48 7595 7607 10.1021/bi900600b 19627112 Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase. 2009 10.2210/pdb2kmn/pdb pdb_00002kmn 16661.125 Peptide deformylase 3.5.1.88 1 man polymer 65.409 ZINC ION 1 syn non-polymer 385.498 ACTINONIN 1 syn non-polymer PDF, Polypeptide deformylase no no SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEK SGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLS SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEK SGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLS A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample def, fms, b3287, JW3248 83333 Escherichia coli K-12 562 Escherichia coli BL21(DE3) Plasmid pET22 Solution Structure of Peptide Deformylase complexed with Actinonin database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Database references Derived calculations 1 0 2009-08-25 1 1 2011-07-13 1 2 2022-03-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Backbone and side chain assignments of peptide deformylase complexed with actinonin BMRB Y RCSB 2009-08-01 REL REL ZN ZINC ION BB2 ACTINONIN structures with the lowest energy 100 20 2D 1H-15N HSQC 2D 1H-13C HSQC 3D CBCA(CO)NH 3D HNCO 3D HNCACB 3D HBHA(CO)NH 3D HCCH-TOCSY 3D HCCH-COSY 3D 1H-15N TOCSY 3D 1H-15N NOESY 3D HNHA 3D HNHB 3D C(CO)NH 0.6-1.0 mM [U-100% 13C; U-100% 15N] 1.2 mM 10 7.2 ambient 310 K simulated annealing 1 lowest energy 0.6-1.0 mM [U-100% 13C; U-100% 15N] Protein-1, 1.2 mM ACTINONIN-2, 90% H2O/10% D2O 90% H2O/10% D2O Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax data analysis NMRPipe Johnson, One Moon Scientific data analysis NMRView Johnson, One Moon Scientific chemical shift assignment NMRView Brunger, Adams, Clore, Gros, Nilges and Read structure solution CNS Brunger, Adams, Clore, Gros, Nilges and Read refinement CNS 600 Bruker DMX Bruker DMX 800 Bruker DMX Bruker DMX 600 Bruker DRX Bruker DRX ZN 148 2 ZN ZN 148 A BB2 149 3 BB2 BB2 149 A SER 1 n 1 SER 1 A VAL 2 n 2 VAL 2 A LEU 3 n 3 LEU 3 A GLN 4 n 4 GLN 4 A VAL 5 n 5 VAL 5 A LEU 6 n 6 LEU 6 A HIS 7 n 7 HIS 7 A ILE 8 n 8 ILE 8 A PRO 9 n 9 PRO 9 A ASP 10 n 10 ASP 10 A GLU 11 n 11 GLU 11 A ARG 12 n 12 ARG 12 A LEU 13 n 13 LEU 13 A ARG 14 n 14 ARG 14 A LYS 15 n 15 LYS 15 A VAL 16 n 16 VAL 16 A ALA 17 n 17 ALA 17 A LYS 18 n 18 LYS 18 A PRO 19 n 19 PRO 19 A VAL 20 n 20 VAL 20 A GLU 21 n 21 GLU 21 A GLU 22 n 22 GLU 22 A VAL 23 n 23 VAL 23 A ASN 24 n 24 ASN 24 A ALA 25 n 25 ALA 25 A GLU 26 n 26 GLU 26 A ILE 27 n 27 ILE 27 A GLN 28 n 28 GLN 28 A ARG 29 n 29 ARG 29 A ILE 30 n 30 ILE 30 A VAL 31 n 31 VAL 31 A ASP 32 n 32 ASP 32 A ASP 33 n 33 ASP 33 A MET 34 n 34 MET 34 A PHE 35 n 35 PHE 35 A GLU 36 n 36 GLU 36 A THR 37 n 37 THR 37 A MET 38 n 38 MET 38 A TYR 39 n 39 TYR 39 A ALA 40 n 40 ALA 40 A GLU 41 n 41 GLU 41 A GLU 42 n 42 GLU 42 A GLY 43 n 43 GLY 43 A ILE 44 n 44 ILE 44 A GLY 45 n 45 GLY 45 A LEU 46 n 46 LEU 46 A ALA 47 n 47 ALA 47 A ALA 48 n 48 ALA 48 A THR 49 n 49 THR 49 A GLN 50 n 50 GLN 50 A VAL 51 n 51 VAL 51 A ASP 52 n 52 ASP 52 A ILE 53 n 53 ILE 53 A HIS 54 n 54 HIS 54 A GLN 55 n 55 GLN 55 A ARG 56 n 56 ARG 56 A ILE 57 n 57 ILE 57 A ILE 58 n 58 ILE 58 A VAL 59 n 59 VAL 59 A ILE 60 n 60 ILE 60 A ASP 61 n 61 ASP 61 A VAL 62 n 62 VAL 62 A SER 63 n 63 SER 63 A GLU 64 n 64 GLU 64 A ASN 65 n 65 ASN 65 A ARG 66 n 66 ARG 66 A ASP 67 n 67 ASP 67 A GLU 68 n 68 GLU 68 A ARG 69 n 69 ARG 69 A LEU 70 n 70 LEU 70 A VAL 71 n 71 VAL 71 A LEU 72 n 72 LEU 72 A ILE 73 n 73 ILE 73 A ASN 74 n 74 ASN 74 A PRO 75 n 75 PRO 75 A GLU 76 n 76 GLU 76 A LEU 77 n 77 LEU 77 A LEU 78 n 78 LEU 78 A GLU 79 n 79 GLU 79 A LYS 80 n 80 LYS 80 A SER 81 n 81 SER 81 A GLY 82 n 82 GLY 82 A GLU 83 n 83 GLU 83 A THR 84 n 84 THR 84 A GLY 85 n 85 GLY 85 A ILE 86 n 86 ILE 86 A GLU 87 n 87 GLU 87 A GLU 88 n 88 GLU 88 A GLY 89 n 89 GLY 89 A CYS 90 n 90 CYS 90 A LEU 91 n 91 LEU 91 A SER 92 n 92 SER 92 A ILE 93 n 93 ILE 93 A PRO 94 n 94 PRO 94 A GLU 95 n 95 GLU 95 A GLN 96 n 96 GLN 96 A ARG 97 n 97 ARG 97 A ALA 98 n 98 ALA 98 A LEU 99 n 99 LEU 99 A VAL 100 n 100 VAL 100 A PRO 101 n 101 PRO 101 A ARG 102 n 102 ARG 102 A ALA 103 n 103 ALA 103 A GLU 104 n 104 GLU 104 A LYS 105 n 105 LYS 105 A VAL 106 n 106 VAL 106 A LYS 107 n 107 LYS 107 A ILE 108 n 108 ILE 108 A ARG 109 n 109 ARG 109 A ALA 110 n 110 ALA 110 A LEU 111 n 111 LEU 111 A ASP 112 n 112 ASP 112 A ARG 113 n 113 ARG 113 A ASP 114 n 114 ASP 114 A GLY 115 n 115 GLY 115 A LYS 116 n 116 LYS 116 A PRO 117 n 117 PRO 117 A PHE 118 n 118 PHE 118 A GLU 119 n 119 GLU 119 A LEU 120 n 120 LEU 120 A GLU 121 n 121 GLU 121 A ALA 122 n 122 ALA 122 A ASP 123 n 123 ASP 123 A GLY 124 n 124 GLY 124 A LEU 125 n 125 LEU 125 A LEU 126 n 126 LEU 126 A ALA 127 n 127 ALA 127 A ILE 128 n 128 ILE 128 A CYS 129 n 129 CYS 129 A ILE 130 n 130 ILE 130 A GLN 131 n 131 GLN 131 A HIS 132 n 132 HIS 132 A GLU 133 n 133 GLU 133 A MET 134 n 134 MET 134 A ASP 135 n 135 ASP 135 A HIS 136 n 136 HIS 136 A LEU 137 n 137 LEU 137 A VAL 138 n 138 VAL 138 A GLY 139 n 139 GLY 139 A LYS 140 n 140 LYS 140 A LEU 141 n 141 LEU 141 A PHE 142 n 142 PHE 142 A MET 143 n 143 MET 143 A ASP 144 n 144 ASP 144 A TYR 145 n 145 TYR 145 A LEU 146 n 146 LEU 146 A SER 147 n 147 SER 147 A author_defined_assembly 1 monomeric A CYS 90 A SG CYS 90 1_555 A ZN 148 B ZN ZN 1_555 A HIS 132 A NE2 HIS 132 1_555 93.9 A CYS 90 A SG CYS 90 1_555 A ZN 148 B ZN ZN 1_555 A HIS 136 A NE2 HIS 136 1_555 86.8 A HIS 132 A NE2 HIS 132 1_555 A ZN 148 B ZN ZN 1_555 A HIS 136 A NE2 HIS 136 1_555 123.9 A CYS 90 A SG CYS 90 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C O4 BB2 1_555 95.6 A HIS 132 A NE2 HIS 132 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C O4 BB2 1_555 116.0 A HIS 136 A NE2 HIS 136 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C O4 BB2 1_555 119.8 A CYS 90 A SG CYS 90 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C N1 BB2 1_555 139.4 A HIS 132 A NE2 HIS 132 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C N1 BB2 1_555 75.8 A HIS 136 A NE2 HIS 136 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C N1 BB2 1_555 131.8 A BB2 149 C O4 BB2 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C N1 BB2 1_555 57.3 A CYS 90 A SG CYS 90 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C O2 BB2 1_555 164.1 A HIS 132 A NE2 HIS 132 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C O2 BB2 1_555 96.5 A HIS 136 A NE2 HIS 136 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C O2 BB2 1_555 97.2 A BB2 149 C O4 BB2 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C O2 BB2 1_555 69.0 A BB2 149 C N1 BB2 1_555 A ZN 148 B ZN ZN 1_555 A BB2 149 C O2 BB2 1_555 34.6 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N LEU 46 A N LEU 46 A O VAL 59 A O VAL 59 A N ILE 60 A N ILE 60 A O LEU 70 A O LEU 70 A N THR 84 A N THR 84 A O ARG 102 A O ARG 102 A N VAL 106 A N VAL 106 A O ALA 122 A O ALA 122 1 A A HG2 H27 GLU BB2 88 149 1.12 1 A A HG22 HA THR LEU 49 137 1.22 1 A A HB HB2 ILE LEU 60 70 1.25 1 A A HB2 HE2 LEU MET 77 134 1.25 1 A A HG13 HH21 VAL ARG 100 102 1.25 1 A A HB3 H91 CYS BB2 129 149 1.26 1 A A HB2 HD23 LEU LEU 6 13 1.26 1 A A HB3 HG ASP LEU 10 13 1.27 1 A A HD21 HD12 ASN ILE 24 27 1.28 1 A A HG21 HG23 ILE VAL 44 62 1.28 1 A A HB HG ILE LEU 73 111 1.28 1 A A HD23 H171 LEU BB2 91 149 1.31 1 A A HD13 H251 ILE BB2 44 149 1.33 1 A A HD12 H173 LEU BB2 91 149 1.34 1 A A HG2 HD13 GLU LEU 41 91 1.34 2 A A HG23 HD2 ILE PRO 93 94 1.07 2 A A HD22 HE LEU ARG 78 109 1.20 2 A A HG2 H27 GLU BB2 88 149 1.21 2 A A HG2 HD12 GLU LEU 41 91 1.22 2 A A HD2 HB2 LYS GLU 107 121 1.24 2 A A HD11 H173 LEU BB2 91 149 1.26 2 A A HB HG ILE LEU 73 111 1.27 2 A A HD12 HB2 ILE LEU 58 72 1.28 2 A A HD12 HG LEU LEU 46 91 1.28 2 A A HE3 HB2 MET ASP 38 61 1.28 2 A A HG23 HG22 ILE VAL 44 62 1.29 2 A A HB2 HE2 LEU MET 77 134 1.29 2 A A HD22 HG13 LEU VAL 3 51 1.30 2 A A HD13 HD2 LEU LYS 77 80 1.31 2 A A HB3 HG ASP LEU 10 13 1.31 2 A A HB HB2 ILE LEU 60 70 1.31 2 A A HZ2 HB3 LYS ASP 105 123 1.31 2 A A HB2 HD13 ASN ILE 24 27 1.32 2 A A HD21 H171 LEU BB2 91 149 1.32 2 A A HB3 HD21 ALA LEU 122 126 1.33 2 A A HB2 HD21 LEU LEU 6 13 1.34 3 A A H HD13 ASN ILE 24 27 1.00 3 A A HD13 HB2 ILE LEU 58 72 1.02 3 A A HG13 H VAL SER 62 63 1.06 3 A A HD13 HG LEU LEU 46 91 1.09 3 A A HB2 HE2 LEU MET 77 134 1.09 3 A A HG2 H27 GLU BB2 88 149 1.10 3 A A HG21 HD2 ILE PRO 93 94 1.11 3 A A HZ1 HB3 LYS ASP 105 123 1.13 3 A A HB3 H112 CYS BB2 129 149 1.14 3 A A HB HB2 ILE LEU 60 70 1.15 3 A A HD2 H81 HIS BB2 132 149 1.18 3 A A HH11 HG23 ARG ILE 102 128 1.24 3 A A HB HG ILE LEU 73 111 1.24 3 A A HA3 H113 GLY BB2 45 149 1.24 3 A A HG2 HD12 GLU LEU 41 91 1.26 3 A A HB3 HD23 ALA LEU 122 126 1.27 3 A A HD12 HE3 LEU LYS 77 80 1.29 3 A A HD11 HB LEU VAL 3 51 1.29 3 A A HE3 HB2 MET ASP 38 61 1.32 3 A A HG2 HD23 GLU LEU 41 91 1.34 3 A A HD2 ZN HIS ZN 136 148 1.50 4 A A HD11 H111 ILE BB2 60 149 1.11 4 A A HG21 HD2 ILE PRO 93 94 1.13 4 A A HG2 H27 GLU BB2 88 149 1.17 4 A A HD13 H173 LEU BB2 91 149 1.18 4 A A HD12 HB2 ILE LEU 58 72 1.18 4 A A HG2 HD11 GLU LEU 41 91 1.21 4 A A HB3 HG ASP LEU 10 13 1.24 4 A A HB HB2 ILE LEU 60 70 1.26 4 A A H HD11 ASN ILE 24 27 1.28 4 A A HG22 HG22 ILE VAL 44 62 1.29 4 A A HD22 HG13 LEU VAL 46 51 1.30 4 A A HB HG ILE LEU 73 111 1.31 4 A A HB2 HD21 LEU LEU 6 13 1.32 4 A A HD21 H171 LEU BB2 91 149 1.33 5 A A HD21 HD12 ASN ILE 24 27 1.10 5 A A HG HA SER GLU 63 68 1.16 5 A A HG22 HB3 VAL PHE 100 142 1.21 5 A A HG3 H27 GLU BB2 88 149 1.22 5 A A HE3 HB2 MET ASP 38 61 1.23 5 A A HB3 HD12 ALA LEU 122 126 1.27 5 A A HH HA TYR ARG 39 69 1.28 5 A A HB HG ILE LEU 73 111 1.29 5 A A HB2 HD22 LEU LEU 6 13 1.33 6 A A HG2 H27 GLU BB2 88 149 1.12 6 A A HG22 HD2 ILE PRO 93 94 1.14 6 A A HB2 HD21 LEU LEU 6 13 1.21 6 A A HD12 H173 LEU BB2 91 149 1.22 6 A A HD12 HG LEU LEU 46 91 1.23 6 A A HE3 HB2 MET ASP 38 61 1.23 6 A A HB HB2 ILE LEU 60 70 1.25 6 A A HB HG ILE LEU 73 111 1.25 6 A A HB2 HD12 ASN ILE 24 27 1.25 6 A A HG13 HG2 VAL LYS 138 140 1.27 6 A A HG23 HG23 ILE VAL 44 62 1.29 6 A A HB3 HD13 ALA LEU 122 126 1.31 6 A A HA3 H112 GLY BB2 45 149 1.33 6 A A HG3 HD13 GLU ILE 26 27 1.33 6 A A HD2 HB2 LYS GLU 107 121 1.34 7 A A HG22 HD2 ILE PRO 93 94 1.11 7 A A HG2 HD22 GLU LEU 41 91 1.14 7 A A HD23 HZ2 LEU LYS 77 80 1.14 7 A A HH11 H232 ARG BB2 97 149 1.17 7 A A HE3 HB2 MET ASP 38 61 1.20 7 A A HB3 HG ASP LEU 10 13 1.21 7 A A HD2 HB2 LYS GLU 107 121 1.22 7 A A HG2 H27 GLU BB2 88 149 1.23 7 A A HB2 H112 CYS BB2 129 149 1.24 7 A A HD12 HB2 ILE LEU 58 72 1.26 7 A A HB2 HD21 LEU LEU 6 13 1.27 7 A A HG13 HD11 ILE LEU 73 111 1.28 7 A A HB HG ILE LEU 73 111 1.28 7 A A HD21 HD13 ASN ILE 24 27 1.29 7 A A HB2 HE2 LEU MET 77 134 1.29 7 A A HG22 HG21 ILE VAL 44 62 1.30 7 A A HD13 H251 ILE BB2 44 149 1.32 7 A A HG1 HD11 THR ILE 84 128 1.33 7 A A HD11 HB LEU VAL 3 51 1.33 7 A A HG12 HG2 VAL LYS 138 140 1.33 7 A A HG3 HB2 MET LEU 38 46 1.35 7 A A ZN HO2 ZN BB2 148 149 1.47 8 A A H HD11 ASN ILE 24 27 1.07 8 A A HZ1 HB3 LYS ASP 105 123 1.08 8 A A HG21 HG2 THR GLU 84 104 1.14 8 A A HD23 HE LEU ARG 78 109 1.17 8 A A HD22 HZ2 LEU LYS 77 80 1.17 8 A A HG2 H27 GLU BB2 88 149 1.20 8 A A HG2 HD11 GLU LEU 41 91 1.21 8 A A HB HB2 ILE LEU 60 70 1.25 8 A A HG21 HG23 ILE VAL 44 62 1.30 8 A A HE3 HB2 MET ASP 38 61 1.30 8 A A HD12 HG LEU LEU 46 91 1.30 8 A A HB HG ILE LEU 73 111 1.32 8 A A HB2 H112 CYS BB2 129 149 1.33 9 A A H HD13 ASN ILE 24 27 1.00 9 A A HD11 HZ1 LEU LYS 77 80 1.11 9 A A HD13 H251 ILE BB2 44 149 1.19 9 A A HB2 HD22 LEU LEU 6 13 1.21 9 A A HG2 H27 GLU BB2 88 149 1.21 9 A A HD2 HB2 LYS GLU 107 121 1.22 9 A A HD12 HG LEU LEU 46 91 1.23 9 A A HD11 H173 LEU BB2 91 149 1.23 9 A A HG2 HD12 GLU LEU 41 91 1.28 9 A A HB3 HG ASP LEU 10 13 1.30 9 A A HG21 HG22 ILE VAL 44 62 1.31 9 A A HB HB2 ILE LEU 60 70 1.32 9 A A HB HG ILE LEU 73 111 1.32 9 A A HD21 H171 LEU BB2 91 149 1.32 9 A A HE2 HH11 PHE ARG 35 113 1.32 9 A A HE3 HB2 MET ASP 38 61 1.34 10 A A HD11 HG LEU SER 13 92 1.08 10 A A HG23 HD2 ILE PRO 93 94 1.09 10 A A HG1 HD11 THR ILE 84 128 1.16 10 A A HG2 H27 GLU BB2 88 149 1.17 10 A A HG2 HD21 GLU LEU 41 91 1.20 10 A A HB3 HD12 ALA LEU 122 126 1.22 10 A A HE3 HB2 MET ASP 38 61 1.22 10 A A HD23 HG13 LEU VAL 3 51 1.22 10 A A HG2 HD13 ARG ILE 102 128 1.25 10 A A HB2 HD23 LEU LEU 6 13 1.26 10 A A HB HG ILE LEU 73 111 1.27 10 A A HG22 HB3 VAL PHE 100 142 1.28 10 A A HG23 HG21 ILE VAL 44 62 1.29 10 A A HB HB2 ILE LEU 60 70 1.32 11 A A H HD11 ASN ILE 24 27 1.02 11 A A HB2 HE2 LEU MET 77 134 1.12 11 A A HE3 HB2 MET ASP 38 61 1.16 11 A A HD13 H251 ILE BB2 44 149 1.18 11 A A HG2 H27 GLU BB2 88 149 1.19 11 A A HB2 HD22 LEU LEU 6 13 1.21 11 A A HD2 HB2 LYS GLU 107 121 1.21 11 A A HG2 HD13 GLU LEU 41 91 1.23 11 A A HD13 HB2 ILE LEU 58 72 1.25 11 A A HD12 H173 LEU BB2 91 149 1.25 11 A A HG23 HG VAL CYS 62 129 1.27 11 A A HG23 HG22 ILE VAL 44 62 1.28 11 A A HB3 HG ASP LEU 10 13 1.29 11 A A HD21 H171 LEU BB2 91 149 1.29 11 A A HB HG ILE LEU 73 111 1.29 11 A A HD12 HG LEU LEU 46 91 1.33 11 A A HD2 ZN HIS ZN 136 148 1.59 12 A A HB2 HD11 CYS ILE 90 93 1.08 12 A A HE3 HB2 MET ASP 38 61 1.16 12 A A HB2 HE2 LEU MET 77 134 1.17 12 A A HB2 HD23 LEU LEU 6 13 1.22 12 A A HD2 HB2 LYS GLU 107 121 1.27 12 A A HG13 HD12 ILE LEU 73 111 1.27 12 A A HG2 H27 GLU BB2 88 149 1.27 12 A A HD21 HD23 LEU LEU 72 120 1.28 12 A A HG13 HB3 VAL PHE 100 142 1.28 12 A A HG21 HG23 ILE VAL 44 62 1.30 12 A A HB HG ILE LEU 73 111 1.32 12 A A HH O TYR GLU 39 68 1.53 12 A A HD2 ZN HIS ZN 136 148 1.58 13 A A HD21 HE LEU ARG 78 109 1.00 13 A A HG2 HD23 GLU LEU 41 91 1.12 13 A A HB2 HD12 ASN ILE 24 27 1.22 13 A A HG2 H27 GLU BB2 88 149 1.23 13 A A HG2 HD13 ARG ILE 102 128 1.25 13 A A HB HG ILE LEU 73 111 1.26 13 A A HB HB2 ILE LEU 60 70 1.30 13 A A HB2 H112 CYS BB2 129 149 1.32 13 A A HH HA TYR ARG 39 69 1.34 14 A A HZ1 HB2 LYS HIS 15 54 1.05 14 A A HD21 HD12 ASN ILE 24 27 1.10 14 A A HG2 HD22 GLU LEU 41 91 1.12 14 A A HB2 HE2 LEU MET 77 134 1.17 14 A A HH11 H232 ARG BB2 97 149 1.18 14 A A HG2 H27 GLU BB2 88 149 1.21 14 A A HB2 HD23 LEU LEU 6 13 1.23 14 A A HB HB2 ILE LEU 60 70 1.23 14 A A HE3 HB2 MET ASP 38 61 1.24 14 A A HG23 HG23 ILE VAL 44 62 1.28 14 A A HB HG ILE LEU 73 111 1.29 14 A A HG21 HD2 ILE PRO 93 94 1.29 14 A A HD12 HB2 ILE LEU 58 72 1.29 14 A A HB3 HG ASP LEU 10 13 1.32 14 A A HD2 HB2 LYS GLU 107 121 1.32 14 A A HG11 HG2 VAL LYS 138 140 1.34 14 A A HD2 ZN HIS ZN 136 148 1.59 15 A A HG22 HA THR LEU 49 137 1.03 15 A A HB2 HD12 ASN ILE 24 27 1.04 15 A A HG23 HD2 ILE PRO 93 94 1.10 15 A A HD11 H173 LEU BB2 91 149 1.10 15 A A HG2 H27 GLU BB2 88 149 1.14 15 A A HG2 HD12 GLU LEU 41 91 1.21 15 A A HD11 HG2 ILE PRO 58 75 1.22 15 A A HG21 HB3 VAL PHE 100 142 1.23 15 A A HB HB2 ILE LEU 60 70 1.23 15 A A HD11 H111 ILE BB2 60 149 1.30 15 A A HD12 HE3 LEU LYS 77 80 1.30 15 A A HE3 HB2 MET ASP 38 61 1.32 15 A A HB3 HD13 ALA LEU 122 126 1.33 15 A A HD11 HG LEU LEU 46 91 1.33 15 A A HG21 HG23 ILE VAL 44 62 1.34 15 A A HB HG ILE LEU 73 111 1.34 16 A A HG2 HH22 GLU ARG 26 29 0.96 16 A A HE HG21 ARG ILE 102 128 1.07 16 A A HB3 H112 CYS BB2 129 149 1.10 16 A A HG21 HD2 ILE PRO 93 94 1.12 16 A A HG2 HE2 PRO TYR 101 145 1.22 16 A A HE3 HB2 MET ASP 38 61 1.24 16 A A HG2 H27 GLU BB2 88 149 1.25 16 A A HG23 HB3 VAL PHE 100 142 1.26 16 A A HD21 HD12 ASN ILE 24 27 1.28 16 A A HE HD13 ARG ILE 102 128 1.29 16 A A HA3 H101 GLY BB2 45 149 1.30 16 A A HE2 HD1 LYS HIS 15 54 1.30 16 A A HG21 HG22 ILE VAL 44 62 1.30 16 A A HD2 HB2 LYS GLU 107 121 1.31 16 A A HB HG ILE LEU 73 111 1.34 16 A A HB3 HD13 ALA LEU 122 126 1.35 16 A A HD21 HG3 LEU ARG 78 109 1.35 17 A A HB2 HD12 ASN ILE 24 27 1.03 17 A A HG21 HD2 ILE PRO 93 94 1.07 17 A A HD12 H173 LEU BB2 91 149 1.12 17 A A HE HG2 ARG GLU 109 119 1.15 17 A A HB HB2 ILE LEU 60 70 1.16 17 A A HG2 H27 GLU BB2 88 149 1.20 17 A A HG2 HD13 GLU LEU 41 91 1.22 17 A A HB3 HD13 ALA LEU 122 126 1.24 17 A A HH21 HG21 ARG VAL 56 138 1.27 17 A A HD11 HG LEU LEU 46 91 1.28 17 A A HB2 HE2 LEU MET 77 134 1.28 17 A A HG13 HD13 ILE LEU 73 111 1.30 17 A A HG22 HD11 VAL LEU 23 111 1.31 17 A A HE2 HH11 PHE ARG 35 113 1.34 17 A A HD12 HD11 ILE LEU 8 13 1.35 18 A A HB2 HD12 ASN ILE 24 27 1.04 18 A A HG21 HD2 ILE PRO 93 94 1.06 18 A A HB3 HD3 GLU LYS 79 107 1.09 18 A A HD12 HD13 ILE ILE 53 57 1.11 18 A A HG2 H27 GLU BB2 88 149 1.12 18 A A HB HB2 ILE LEU 60 70 1.18 18 A A HD13 H251 ILE BB2 44 149 1.18 18 A A HD12 H173 LEU BB2 91 149 1.21 18 A A HD13 HG LEU LEU 46 91 1.22 18 A A HG13 HD11 ILE LEU 73 111 1.22 18 A A HB2 HD23 LEU LEU 6 13 1.23 18 A A HB3 HG ASP LEU 10 13 1.26 18 A A HG13 HG2 VAL LYS 138 140 1.27 18 A A HD3 HD2 PRO ARG 19 56 1.29 18 A A HG2 HD13 GLU LEU 41 91 1.29 18 A A HG23 HG23 ILE VAL 44 62 1.29 18 A A HB HG ILE LEU 73 111 1.30 18 A A HB2 HE2 LEU MET 77 134 1.31 18 A A HD22 H171 LEU BB2 91 149 1.34 18 A A HE22 HO2 GLN BB2 50 149 1.34 19 A A HB2 HD12 ASN ILE 24 27 1.12 19 A A HG2 H27 GLU BB2 88 149 1.17 19 A A HB HB2 ILE LEU 60 70 1.20 19 A A HB2 HE2 LEU MET 77 134 1.21 19 A A HE3 HB2 MET ASP 38 61 1.21 19 A A HG2 HD13 GLU LEU 41 91 1.26 19 A A HG21 HB2 VAL ARG 71 113 1.27 19 A A HD12 H173 LEU BB2 91 149 1.28 19 A A HD12 HG LEU SER 13 92 1.29 19 A A HB HG ILE LEU 73 111 1.31 19 A A HG21 H113 ILE BB2 60 149 1.32 19 A A HB3 HD13 ALA LEU 122 126 1.32 19 A A HD12 HG LEU LEU 46 91 1.33 19 A A HG23 HD2 ILE PRO 93 94 1.34 19 A A HB2 HH12 ALA ARG 25 29 1.34 19 A A HD2 ZN HIS ZN 136 148 1.59 20 A A HD22 HE LEU ARG 78 109 1.01 20 A A HD21 HD12 ASN ILE 24 27 1.05 20 A A HA HZ1 ARG LYS 12 15 1.12 20 A A HD11 H111 ILE BB2 60 149 1.14 20 A A HG2 H27 GLU BB2 88 149 1.22 20 A A HB2 HD21 LEU LEU 6 13 1.22 20 A A HB2 HE2 LEU MET 77 134 1.23 20 A A HE3 HB2 MET ASP 38 61 1.26 20 A A HD2 HB2 LYS GLU 107 121 1.28 20 A A HD11 HG LEU LEU 46 91 1.29 20 A A HB2 HD13 CYS ILE 90 93 1.30 20 A A HB3 HG ASP LEU 10 13 1.30 20 A A HB3 HD22 ALA LEU 122 126 1.32 20 A A HB HG ILE LEU 73 111 1.33 20 A A HD11 H173 LEU BB2 91 149 1.33 20 A A HB HB2 ILE LEU 60 70 1.35 20 A A HG22 HG22 ILE VAL 44 62 1.35 20 A A HG2 HD12 GLU LEU 41 91 1.35 20 A A HD2 ZN HIS ZN 136 148 1.55 1 A LEU 3 -80.46 -147.47 1 A ALA 48 -26.82 -57.24 1 A ASP 52 80.13 25.51 1 A ARG 56 -64.67 75.63 1 A ASP 61 -145.12 31.86 1 A SER 63 -55.80 65.75 1 A ASN 65 -163.28 -139.47 1 A ARG 69 -179.94 63.77 1 A PRO 94 -72.40 49.25 2 A LEU 3 -79.10 -143.43 2 A PRO 9 -92.68 52.48 2 A ARG 56 -63.01 69.03 2 A SER 63 -37.56 81.19 2 A ASN 65 -165.99 -141.87 2 A ARG 66 -83.57 38.48 2 A GLU 68 -111.27 61.78 3 A LEU 3 -83.10 -148.76 3 A PRO 9 -93.17 52.13 3 A ARG 56 -63.13 68.65 3 A ASN 65 -161.99 -66.16 3 A ARG 66 -130.99 -36.75 3 A ARG 69 173.65 69.20 3 A PRO 94 -63.05 -148.42 4 A ASP 52 75.36 30.04 4 A ARG 56 -64.26 70.74 4 A SER 63 -38.05 80.50 4 A ASN 65 -164.64 -132.99 4 A ARG 69 170.67 76.08 4 A PRO 94 -76.46 49.75 5 A PRO 9 -91.86 50.20 5 A ASP 52 79.35 31.52 5 A ARG 56 -62.74 69.06 5 A ASN 65 -165.88 -131.80 5 A ARG 69 -176.62 65.73 5 A PRO 94 -75.20 48.43 5 A GLU 95 82.88 9.27 6 A LEU 3 -79.01 -159.30 6 A ALA 48 -29.85 -54.59 6 A ARG 56 -64.11 68.62 6 A ASP 61 -142.58 28.56 6 A SER 63 -37.05 84.59 6 A ASN 65 -164.10 -85.76 6 A ARG 69 171.22 70.53 6 A PRO 94 -61.75 -144.43 7 A LEU 3 -79.68 -158.69 7 A ALA 48 -29.31 -56.16 7 A ASP 52 77.13 35.27 7 A ARG 56 -62.81 74.55 7 A SER 63 -39.95 76.38 7 A ASN 65 -164.41 -136.14 7 A ARG 69 172.48 76.28 7 A PRO 94 -78.24 47.67 7 A GLU 95 80.22 4.66 8 A PRO 9 -92.35 51.19 8 A ALA 48 -28.51 -57.99 8 A ARG 56 -61.79 72.52 8 A SER 63 -42.42 81.51 8 A ARG 66 -161.34 -91.13 8 A GLU 68 71.78 101.38 8 A ARG 69 175.20 64.11 8 A PRO 94 -75.68 47.08 9 A ALA 48 -27.21 -56.82 9 A ASP 52 77.51 33.06 9 A ARG 56 -64.37 72.46 9 A SER 63 -34.10 89.77 9 A ASN 65 -168.16 -85.19 9 A ARG 69 175.39 71.79 9 A PRO 94 -73.32 48.93 10 A LEU 3 -79.09 -141.25 10 A PRO 9 -92.14 51.68 10 A ARG 56 -61.78 68.10 10 A ASP 61 -141.82 37.78 10 A SER 63 -34.08 86.87 10 A ASN 65 -164.75 -74.58 10 A ARG 69 173.89 66.76 10 A PRO 94 -62.63 -146.54 11 A ALA 48 -27.06 -55.74 11 A ASP 52 77.43 34.05 11 A ARG 56 -65.13 72.38 11 A SER 63 -34.42 85.58 11 A ASN 65 -165.17 -79.04 11 A ARG 69 175.02 68.61 11 A PRO 94 -73.10 48.48 12 A ASN 24 -105.76 -168.66 12 A ASP 52 78.96 32.37 12 A ARG 56 -63.34 70.82 12 A SER 63 -38.02 83.28 12 A ASN 65 -163.87 -127.97 13 A PRO 9 -98.18 55.48 13 A ASP 52 77.75 32.40 13 A ARG 56 -62.84 70.69 13 A SER 63 -35.29 89.32 13 A ASN 65 -165.60 -76.51 13 A ARG 69 178.23 68.83 13 A PRO 94 -75.36 47.73 14 A ALA 48 -29.70 -56.15 14 A ASP 52 76.53 32.89 14 A ARG 56 -65.37 72.40 14 A ASP 61 -146.11 34.12 14 A SER 63 -38.26 77.71 14 A ASN 65 -165.51 -84.99 14 A ARG 69 -174.92 62.10 14 A PRO 94 -75.51 47.70 15 A ALA 48 -28.73 -56.76 15 A HIS 54 -75.84 49.18 15 A ARG 56 -62.46 75.14 15 A ASP 61 -140.16 27.60 15 A SER 63 -35.95 85.40 15 A ASN 65 -133.84 -67.10 15 A ARG 66 -133.27 -42.86 15 A ARG 69 177.17 66.76 15 A PRO 94 -71.96 44.84 16 A PRO 9 -93.49 54.12 16 A ASP 52 79.11 31.45 16 A ARG 56 -64.66 69.04 16 A SER 63 -36.33 78.84 16 A ASN 65 -167.25 -126.30 16 A ARG 69 177.12 71.84 16 A PRO 94 -74.87 48.09 17 A LEU 3 -79.87 -169.51 17 A PRO 9 -93.22 52.38 17 A ARG 56 -65.02 70.99 17 A ASP 61 -145.29 39.84 17 A SER 63 -55.35 74.70 17 A ASN 65 -122.01 -72.86 17 A ASP 67 -161.25 116.62 17 A LEU 91 -48.62 -17.31 17 A PRO 94 -62.11 -145.98 18 A LEU 3 -79.53 -161.81 18 A ARG 56 -64.50 66.72 18 A SER 63 -38.88 78.25 18 A ASN 65 -163.30 -138.23 18 A PRO 94 -70.98 49.16 19 A PRO 9 -93.49 51.84 19 A ALA 48 -26.90 -56.50 19 A ARG 56 -59.83 68.34 19 A VAL 62 -79.46 -161.33 19 A ASN 65 -165.84 -119.22 20 A LEU 3 -79.74 -165.97 20 A ALA 48 -28.61 -54.43 20 A ASP 52 77.46 30.07 20 A ARG 56 -64.00 69.30 20 A SER 63 -38.35 81.59 20 A ASN 65 -165.12 -139.98 20 A ARG 69 173.29 72.03 lowest energy, model 1 Solution structure of peptide deformylase complexed with actinonin 1 N N 2 N N 3 N N A ASN 24 A ASN 24 HELX_P A GLU 41 A GLU 41 1 1 18 A THR 49 A THR 49 HELX_P A ASP 52 A ASP 52 5 2 4 A GLY 124 A GLY 124 HELX_P A VAL 138 A VAL 138 1 3 15 A LEU 141 A LEU 141 HELX_P A LEU 146 A LEU 146 5 4 6 metalc 2.029 A CYS 90 A SG CYS 90 1_555 A ZN 148 B ZN ZN 1_555 metalc 2.366 A HIS 132 A NE2 HIS 132 1_555 A ZN 148 B ZN ZN 1_555 metalc 2.377 A HIS 136 A NE2 HIS 136 1_555 A ZN 148 B ZN ZN 1_555 metalc 2.345 A ZN 148 B ZN ZN 1_555 A BB2 149 C O4 BB2 1_555 metalc 2.341 A ZN 148 B ZN ZN 1_555 A BB2 149 C N1 BB2 1_555 metalc 2.335 A ZN 148 B ZN ZN 1_555 A BB2 149 C O2 BB2 1_555 HYDROLASE/ANTIBIOTIC Peptide Deformylase, Actinonin, Hydrolase, Iron, Metal-binding, Protein biosynthesis, HYDROLASE-ANTIBIOTIC COMPLEX A ILE 8 A ILE 8 1 A PRO 9 A PRO 9 -0.31 A ILE 8 A ILE 8 2 A PRO 9 A PRO 9 0.14 A ILE 8 A ILE 8 3 A PRO 9 A PRO 9 0.44 A ILE 8 A ILE 8 4 A PRO 9 A PRO 9 -0.38 A ILE 8 A ILE 8 5 A PRO 9 A PRO 9 0.18 A ILE 8 A ILE 8 6 A PRO 9 A PRO 9 -0.15 A ILE 8 A ILE 8 7 A PRO 9 A PRO 9 -0.33 A ILE 8 A ILE 8 8 A PRO 9 A PRO 9 0.09 A ILE 8 A ILE 8 9 A PRO 9 A PRO 9 -0.57 A ILE 8 A ILE 8 10 A PRO 9 A PRO 9 0.17 A ILE 8 A ILE 8 11 A PRO 9 A PRO 9 -0.32 A ILE 8 A ILE 8 12 A PRO 9 A PRO 9 -0.51 A ILE 8 A ILE 8 13 A PRO 9 A PRO 9 0.29 A ILE 8 A ILE 8 14 A PRO 9 A PRO 9 -0.28 A ILE 8 A ILE 8 15 A PRO 9 A PRO 9 -0.42 A ILE 8 A ILE 8 16 A PRO 9 A PRO 9 0.32 A ILE 8 A ILE 8 17 A PRO 9 A PRO 9 0.20 A ILE 8 A ILE 8 18 A PRO 9 A PRO 9 -0.30 A ILE 8 A ILE 8 19 A PRO 9 A PRO 9 0.24 A ILE 8 A ILE 8 20 A PRO 9 A PRO 9 -0.49 DEF_ECOLI UNP 1 2 P0A6K3 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEK SGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLS 2 148 2KMN 1 147 P0A6K3 A 1 1 147 5 anti-parallel anti-parallel anti-parallel anti-parallel A GLY 45 A GLY 45 A ALA 47 A ALA 47 A ILE 57 A ILE 57 A ILE 60 A ILE 60 A LEU 70 A LEU 70 A GLU 88 A GLU 88 A ALA 98 A ALA 98 A LEU 111 A LEU 111 A PRO 117 A PRO 117 A ASP 123 A ASP 123 BINDING SITE FOR RESIDUE ZN A 148 A ZN 148 Software 5 BINDING SITE FOR RESIDUE BB2 A 149 A BB2 149 Software 17 A GLN 50 A GLN 50 5 1_555 A CYS 90 A CYS 90 5 1_555 A HIS 132 A HIS 132 5 1_555 A HIS 136 A HIS 136 5 1_555 A BB2 149 C BB2 5 1_555 A GLY 43 A GLY 43 17 1_555 A ILE 44 A ILE 44 17 1_555 A GLY 45 A GLY 45 17 1_555 A GLN 50 A GLN 50 17 1_555 A VAL 59 A VAL 59 17 1_555 A ILE 60 A ILE 60 17 1_555 A GLU 87 A GLU 87 17 1_555 A GLU 88 A GLU 88 17 1_555 A GLY 89 A GLY 89 17 1_555 A CYS 90 A CYS 90 17 1_555 A LEU 91 A LEU 91 17 1_555 A ARG 97 A ARG 97 17 1_555 A CYS 129 A CYS 129 17 1_555 A HIS 132 A HIS 132 17 1_555 A GLU 133 A GLU 133 17 1_555 A HIS 136 A HIS 136 17 1_555 A ZN 148 B ZN 17 1_555