0.026042 0.000000 0.000000 0.000000 0.019724 0.000000 0.000000 0.000000 0.009533 0.00000 0.00000 0.00000 Zhao, B. Smith, W.W. Janson, C.A. Abdel-Meguid, S.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 38.400 50.700 104.900 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 C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C15 H30 N5 O5 1 360.429 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE non-polymer 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 H2 O 18.015 WATER non-polymer 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 C11 H12 N2 O2 204.225 y TRYPTOPHAN 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 US Nat.Struct.Biol. NSBIEW 2024 1072-8368 4 109 111 10.1038/nsb0297-109 9033588 Crystal structure of human osteoclast cathepsin K complex with E-64. 1997 10.2210/pdb1atk/pdb pdb_00001atk 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 287 1 MONOCHROMATOR AREA DETECTOR 1995-10-25 SIEMENS GRAPHITE(002) M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE SIEMENS INHIBITOR E-64 COVALENT LINK BETWEEN INHIBITOR ATOM C2 AND THE SULFUR OF CYS 25 23523.480 CATHEPSIN K 3.4.22.38 1 man polymer 360.429 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE 1 syn non-polymer 18.015 water 28 nat water no no APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRG IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNL NHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRG IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNL NHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 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 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 human Homo fall armyworm Spodoptera sample HUMAN OSTEOCLASTS SF21 9606 Homo sapiens SF21 7108 Spodoptera frugiperda BACULOVIRUS 1 2.1 43. VAPOR DIFFUSION 6.2 PROTEIN CRYSTALLIZED FROM 10% PEG 8000, 0.1 M NA/K PHOSPHATE AT PH 6.2 CONTAINING 0.2 M NACL AT ROOM TEMPERATURE BY VAPOR DIFFUSION., vapor diffusion room temp diffrn_source pdbx_database_status database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Other Database references Derived calculations Refinement description 1 0 1998-02-04 1 1 2008-03-24 1 2 2011-07-13 1 3 2018-03-07 1 4 2023-08-02 _diffrn_source.source _pdbx_database_status.process_site _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_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.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1996-12-19 REL E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE HOH water 9PAP PDB ENTRY 9PAP PDB experimental model E64 216 2 E64 E64 216 A HOH 217 3 HOH HOH 217 A HOH 218 3 HOH HOH 218 A HOH 219 3 HOH HOH 219 A HOH 220 3 HOH HOH 220 A HOH 221 3 HOH HOH 221 A HOH 222 3 HOH HOH 222 A HOH 223 3 HOH HOH 223 A HOH 224 3 HOH HOH 224 A HOH 225 3 HOH HOH 225 A HOH 226 3 HOH HOH 226 A HOH 227 3 HOH HOH 227 A HOH 228 3 HOH HOH 228 A HOH 229 3 HOH HOH 229 A HOH 230 3 HOH HOH 230 A HOH 231 3 HOH HOH 231 A HOH 232 3 HOH HOH 232 A HOH 233 3 HOH HOH 233 A HOH 234 3 HOH HOH 234 A HOH 235 3 HOH HOH 235 A HOH 236 3 HOH HOH 236 A HOH 237 3 HOH HOH 237 A HOH 238 3 HOH HOH 238 A HOH 239 3 HOH HOH 239 A HOH 240 3 HOH HOH 240 A HOH 241 3 HOH HOH 241 A HOH 242 3 HOH HOH 242 A HOH 243 3 HOH HOH 243 A HOH 244 3 HOH HOH 244 A ALA 1 n 1 ALA 1 A PRO 2 n 2 PRO 2 A ASP 3 n 3 ASP 3 A SER 4 n 4 SER 4 A VAL 5 n 5 VAL 5 A ASP 6 n 6 ASP 6 A TYR 7 n 7 TYR 7 A ARG 8 n 8 ARG 8 A LYS 9 n 9 LYS 9 A LYS 10 n 10 LYS 10 A GLY 11 n 11 GLY 11 A TYR 12 n 12 TYR 12 A VAL 13 n 13 VAL 13 A THR 14 n 14 THR 14 A PRO 15 n 15 PRO 15 A VAL 16 n 16 VAL 16 A LYS 17 n 17 LYS 17 A ASN 18 n 18 ASN 18 A GLN 19 n 19 GLN 19 A GLY 20 n 20 GLY 20 A GLN 21 n 21 GLN 21 A CYS 22 n 22 CYS 22 A GLY 23 n 23 GLY 23 A SER 24 n 24 SER 24 A CYS 25 n 25 CYS 25 A TRP 26 n 26 TRP 26 A ALA 27 n 27 ALA 27 A PHE 28 n 28 PHE 28 A SER 29 n 29 SER 29 A SER 30 n 30 SER 30 A VAL 31 n 31 VAL 31 A GLY 32 n 32 GLY 32 A ALA 33 n 33 ALA 33 A LEU 34 n 34 LEU 34 A GLU 35 n 35 GLU 35 A GLY 36 n 36 GLY 36 A GLN 37 n 37 GLN 37 A LEU 38 n 38 LEU 38 A LYS 39 n 39 LYS 39 A LYS 40 n 40 LYS 40 A LYS 41 n 41 LYS 41 A THR 42 n 42 THR 42 A GLY 43 n 43 GLY 43 A LYS 44 n 44 LYS 44 A LEU 45 n 45 LEU 45 A LEU 46 n 46 LEU 46 A ASN 47 n 47 ASN 47 A LEU 48 n 48 LEU 48 A SER 49 n 49 SER 49 A PRO 50 n 50 PRO 50 A GLN 51 n 51 GLN 51 A ASN 52 n 52 ASN 52 A LEU 53 n 53 LEU 53 A VAL 54 n 54 VAL 54 A ASP 55 n 55 ASP 55 A CYS 56 n 56 CYS 56 A VAL 57 n 57 VAL 57 A SER 58 n 58 SER 58 A GLU 59 n 59 GLU 59 A ASN 60 n 60 ASN 60 A ASP 61 n 61 ASP 61 A GLY 62 n 62 GLY 62 A CYS 63 n 63 CYS 63 A GLY 64 n 64 GLY 64 A GLY 65 n 65 GLY 65 A GLY 66 n 66 GLY 66 A TYR 67 n 67 TYR 67 A MET 68 n 68 MET 68 A THR 69 n 69 THR 69 A ASN 70 n 70 ASN 70 A ALA 71 n 71 ALA 71 A PHE 72 n 72 PHE 72 A GLN 73 n 73 GLN 73 A TYR 74 n 74 TYR 74 A VAL 75 n 75 VAL 75 A GLN 76 n 76 GLN 76 A LYS 77 n 77 LYS 77 A ASN 78 n 78 ASN 78 A ARG 79 n 79 ARG 79 A GLY 80 n 80 GLY 80 A ILE 81 n 81 ILE 81 A ASP 82 n 82 ASP 82 A SER 83 n 83 SER 83 A GLU 84 n 84 GLU 84 A ASP 85 n 85 ASP 85 A ALA 86 n 86 ALA 86 A TYR 87 n 87 TYR 87 A PRO 88 n 88 PRO 88 A TYR 89 n 89 TYR 89 A VAL 90 n 90 VAL 90 A GLY 91 n 91 GLY 91 A GLN 92 n 92 GLN 92 A GLU 93 n 93 GLU 93 A GLU 94 n 94 GLU 94 A SER 95 n 95 SER 95 A CYS 96 n 96 CYS 96 A MET 97 n 97 MET 97 A TYR 98 n 98 TYR 98 A ASN 99 n 99 ASN 99 A PRO 100 n 100 PRO 100 A THR 101 n 101 THR 101 A GLY 102 n 102 GLY 102 A LYS 103 n 103 LYS 103 A ALA 104 n 104 ALA 104 A ALA 105 n 105 ALA 105 A LYS 106 n 106 LYS 106 A CYS 107 n 107 CYS 107 A ARG 108 n 108 ARG 108 A GLY 109 n 109 GLY 109 A TYR 110 n 110 TYR 110 A ARG 111 n 111 ARG 111 A GLU 112 n 112 GLU 112 A ILE 113 n 113 ILE 113 A PRO 114 n 114 PRO 114 A GLU 115 n 115 GLU 115 A GLY 116 n 116 GLY 116 A ASN 117 n 117 ASN 117 A GLU 118 n 118 GLU 118 A LYS 119 n 119 LYS 119 A ALA 120 n 120 ALA 120 A LEU 121 n 121 LEU 121 A LYS 122 n 122 LYS 122 A ARG 123 n 123 ARG 123 A ALA 124 n 124 ALA 124 A VAL 125 n 125 VAL 125 A ALA 126 n 126 ALA 126 A ARG 127 n 127 ARG 127 A VAL 128 n 128 VAL 128 A GLY 129 n 129 GLY 129 A PRO 130 n 130 PRO 130 A VAL 131 n 131 VAL 131 A SER 132 n 132 SER 132 A VAL 133 n 133 VAL 133 A ALA 134 n 134 ALA 134 A ILE 135 n 135 ILE 135 A ASP 136 n 136 ASP 136 A ALA 137 n 137 ALA 137 A SER 138 n 138 SER 138 A LEU 139 n 139 LEU 139 A THR 140 n 140 THR 140 A SER 141 n 141 SER 141 A PHE 142 n 142 PHE 142 A GLN 143 n 143 GLN 143 A PHE 144 n 144 PHE 144 A TYR 145 n 145 TYR 145 A SER 146 n 146 SER 146 A LYS 147 n 147 LYS 147 A GLY 148 n 148 GLY 148 A VAL 149 n 149 VAL 149 A TYR 150 n 150 TYR 150 A TYR 151 n 151 TYR 151 A ASP 152 n 152 ASP 152 A GLU 153 n 153 GLU 153 A SER 154 n 154 SER 154 A CYS 155 n 155 CYS 155 A ASN 156 n 156 ASN 156 A SER 157 n 157 SER 157 A ASP 158 n 158 ASP 158 A ASN 159 n 159 ASN 159 A LEU 160 n 160 LEU 160 A ASN 161 n 161 ASN 161 A HIS 162 n 162 HIS 162 A ALA 163 n 163 ALA 163 A VAL 164 n 164 VAL 164 A LEU 165 n 165 LEU 165 A ALA 166 n 166 ALA 166 A VAL 167 n 167 VAL 167 A GLY 168 n 168 GLY 168 A TYR 169 n 169 TYR 169 A GLY 170 n 170 GLY 170 A ILE 171 n 171 ILE 171 A GLN 172 n 172 GLN 172 A LYS 173 n 173 LYS 173 A GLY 174 n 174 GLY 174 A ASN 175 n 175 ASN 175 A LYS 176 n 176 LYS 176 A HIS 177 n 177 HIS 177 A TRP 178 n 178 TRP 178 A ILE 179 n 179 ILE 179 A ILE 180 n 180 ILE 180 A LYS 181 n 181 LYS 181 A ASN 182 n 182 ASN 182 A SER 183 n 183 SER 183 A TRP 184 n 184 TRP 184 A GLY 185 n 185 GLY 185 A GLU 186 n 186 GLU 186 A ASN 187 n 187 ASN 187 A TRP 188 n 188 TRP 188 A GLY 189 n 189 GLY 189 A ASN 190 n 190 ASN 190 A LYS 191 n 191 LYS 191 A GLY 192 n 192 GLY 192 A TYR 193 n 193 TYR 193 A ILE 194 n 194 ILE 194 A LEU 195 n 195 LEU 195 A MET 196 n 196 MET 196 A ALA 197 n 197 ALA 197 A ARG 198 n 198 ARG 198 A ASN 199 n 199 ASN 199 A LYS 200 n 200 LYS 200 A ASN 201 n 201 ASN 201 A ASN 202 n 202 ASN 202 A ALA 203 n 203 ALA 203 A CYS 204 n 204 CYS 204 A GLY 205 n 205 GLY 205 A ILE 206 n 206 ILE 206 A ALA 207 n 207 ALA 207 A ASN 208 n 208 ASN 208 A LEU 209 n 209 LEU 209 A ALA 210 n 210 ALA 210 A SER 211 n 211 SER 211 A PHE 212 n 212 PHE 212 A PRO 213 n 213 PRO 213 A LYS 214 n 214 LYS 214 A MET 215 n 215 MET 215 A author_defined_assembly 1 monomeric 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 O ARG 111 A O ARG 111 A N PHE 212 A N PHE 212 A O VAL 131 A O VAL 131 A N ALA 166 A N ALA 166 A O LEU 165 A O LEU 165 A N LYS 181 A N LYS 181 A O TRP 178 A O TRP 178 A N MET 196 A N MET 196 1 A GLN 21 -90.24 46.54 1 A ARG 79 71.84 38.67 1 A TYR 87 -157.97 73.51 1 A ASN 159 -142.31 56.19 1 A GLN 172 -90.09 -110.70 1 A LYS 200 -113.30 56.62 PARHCSDX.PRO TOPHCSDX.PRO 0.31 0.095 0.215 0.215 2.20 7.00 1061 10052 8.7 84.7 RANDOM 100000. 0.1 1 2. MOLECULAR REPLACEMENT PDB ENTRY 9PAP 7.0 2.20 7.00 89 1852 26 0 1737 0.007 1.51 22.8 1.1 2.3 8 66.4 2.20 25. 1ATK 10418 2. 0.095 0.095 1 14. 3.2 95. 0.19 2.20 2.34 2.94 0.19 2.3 80. data collection XENGEN data reduction XENGEN model building X-PLOR 3.1 refinement X-PLOR 3.1 data scaling XENGEN phasing X-PLOR 3.1 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH THE COVALENT INHIBITOR E-64 1 N N 2 N N 3 N N A TYR 7 A TYR 7 HELX_P A LYS 10 A LYS 10 5 1 4 A CYS 25 A CYS 25 HELX_P A THR 42 A THR 42 1 2 18 A PRO 50 A PRO 50 HELX_P A CYS 56 A CYS 56 1 3 7 A GLY 62 A GLY 62 HELX_P A GLY 64 A GLY 64 5 4 3 A MET 68 A MET 68 HELX_P A ASN 78 A ASN 78 1 5 11 A PRO 100 A PRO 100 HELX_P A GLY 102 A GLY 102 5 6 3 A GLU 118 A GLU 118 HELX_P A ARG 127 A ARG 127 1 7 10 A THR 140 A THR 140 HELX_P A GLN 143 A GLN 143 1 8 4 A ALA 203 A ALA 203 HELX_P A GLY 205 A GLY 205 5 9 3 disulf 2.035 A CYS 22 A SG CYS 22 1_555 A CYS 63 A SG CYS 63 1_555 disulf 2.028 A CYS 56 A SG CYS 56 1_555 A CYS 96 A SG CYS 96 1_555 disulf 2.033 A CYS 155 A SG CYS 155 1_555 A CYS 204 A SG CYS 204 1_555 covale 1.797 none A CYS 25 A SG CYS 25 1_555 A E64 216 B C2 E64 1_555 HYDROLASE HYDROLASE, SULFHYDRYL PROTEINASE CATK_HUMAN UNP 1 1 P43235 MWGLKVLLLPVVSFALYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMNHLGD MTSEEVVQKMTGLKVPLSHSRSNDTLYIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLL NLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVA RVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGI ANLASFPKM 115 329 1ATK 1 215 P43235 A 1 1 215 2 4 anti-parallel anti-parallel anti-parallel anti-parallel A TYR 110 A TYR 110 A GLU 112 A GLU 112 A SER 211 A SER 211 A PRO 213 A PRO 213 A VAL 131 A VAL 131 A ILE 135 A ILE 135 A HIS 162 A HIS 162 A ILE 171 A ILE 171 A LYS 176 A LYS 176 A LYS 181 A LYS 181 A TYR 193 A TYR 193 A ALA 197 A ALA 197 BINDING SITE FOR RESIDUE E64 A 216 A E64 216 Software 17 A SER 4 A SER 4 17 1_655 A GLN 19 A GLN 19 17 1_555 A GLY 23 A GLY 23 17 1_555 A SER 24 A SER 24 17 1_555 A CYS 25 A CYS 25 17 1_555 A TRP 26 A TRP 26 17 1_555 A GLU 59 A GLU 59 17 1_555 A ASN 60 A ASN 60 17 1_555 A ASP 61 A ASP 61 17 1_555 A GLY 65 A GLY 65 17 1_555 A GLY 66 A GLY 66 17 1_555 A TYR 67 A TYR 67 17 1_555 A LEU 160 A LEU 160 17 1_555 A ASN 161 A ASN 161 17 1_555 A HIS 162 A HIS 162 17 1_555 A HOH 225 C HOH 17 1_555 A HOH 232 C HOH 17 1_555 19 P 21 21 21