0.009901 0.000000 0.001675 0.000000 0.019612 0.000000 0.000000 0.000000 0.016232 0.00000 0.00000 0.00000 Lalonde, J.M. Zhao, B. Smith, W.W. Janson, C.A. Desjarlais, R.L. Tomaszek, T.A. Carr, T.J. Thompson, S.K. Yamashita, D.S. Veber, D.F. Abdel-Mequid, S.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 99.60 90.00 101.000 50.990 62.480 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 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 C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C22 H36 N2 O5 408.532 CARBOBENZYLOXY-(L)-LEUCINYL-(L)LEUCINYL METHOXYMETHYLKETONE non-polymer 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 J.Med.Chem. JMCMAR 0151 0022-2623 41 4567 4576 10.1021/jm980249f 9804696 Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites. 1998 10.2210/pdb1bqi/pdb pdb_00001bqi 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 AREA DETECTOR 1995-06 SIEMENS MONOCHROMATOR M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE SIEMENS METHOXYMETHYLKETONE BOUND NON-COVALENTLY IN S'-SUBSITE 23449.346 PAPAIN 1 nat polymer 408.532 CARBOBENZYLOXY-(L)-LEUCINYL-(L)LEUCINYL METHOXYMETHYLKETONE 1 syn non-polymer 18.015 water 42 nat water no no IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 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 papaya Carica sample 3649 Carica papaya 2 3.3 63.62 8.5 pH 8.5 diffrn_source pdbx_database_status pdbx_unobs_or_zero_occ_atoms database_2 pdbx_initial_refinement_model pdbx_unobs_or_zero_occ_atoms struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Advisory Data collection Other Advisory Database references Derived calculations Refinement description 1 0 1999-08-16 1 1 2008-03-24 1 2 2011-07-13 1 3 2018-03-07 1 4 2023-08-09 _diffrn_source.source _pdbx_database_status.process_site _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1998-08-16 REL SBA CARBOBENZYLOXY-(L)-LEUCINYL-(L)LEUCINYL METHOXYMETHYLKETONE HOH water 1PIP PDB ENTRY 1PIP PDB experimental model SBA 300 2 SBA SBA 300 A HOH 400 3 HOH HOH 400 A HOH 404 3 HOH HOH 404 A HOH 405 3 HOH HOH 405 A HOH 406 3 HOH HOH 406 A HOH 409 3 HOH HOH 409 A HOH 410 3 HOH HOH 410 A HOH 411 3 HOH HOH 411 A HOH 413 3 HOH HOH 413 A HOH 414 3 HOH HOH 414 A HOH 415 3 HOH HOH 415 A HOH 416 3 HOH HOH 416 A HOH 418 3 HOH HOH 418 A HOH 421 3 HOH HOH 421 A HOH 422 3 HOH HOH 422 A HOH 426 3 HOH HOH 426 A HOH 429 3 HOH HOH 429 A HOH 435 3 HOH HOH 435 A HOH 436 3 HOH HOH 436 A HOH 441 3 HOH HOH 441 A HOH 443 3 HOH HOH 443 A HOH 444 3 HOH HOH 444 A HOH 450 3 HOH HOH 450 A HOH 451 3 HOH HOH 451 A HOH 453 3 HOH HOH 453 A HOH 454 3 HOH HOH 454 A HOH 455 3 HOH HOH 455 A HOH 456 3 HOH HOH 456 A HOH 457 3 HOH HOH 457 A HOH 468 3 HOH HOH 468 A HOH 469 3 HOH HOH 469 A HOH 484 3 HOH HOH 484 A HOH 487 3 HOH HOH 487 A HOH 490 3 HOH HOH 490 A HOH 501 3 HOH HOH 501 A HOH 502 3 HOH HOH 502 A HOH 504 3 HOH HOH 504 A HOH 505 3 HOH HOH 505 A HOH 506 3 HOH HOH 506 A HOH 507 3 HOH HOH 507 A HOH 508 3 HOH HOH 508 A HOH 510 3 HOH HOH 510 A HOH 511 3 HOH HOH 511 A ILE 1 n 1 ILE 1 A PRO 2 n 2 PRO 2 A GLU 3 n 3 GLU 3 A TYR 4 n 4 TYR 4 A VAL 5 n 5 VAL 5 A ASP 6 n 6 ASP 6 A TRP 7 n 7 TRP 7 A ARG 8 n 8 ARG 8 A GLN 9 n 9 GLN 9 A LYS 10 n 10 LYS 10 A GLY 11 n 11 GLY 11 A ALA 12 n 12 ALA 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 SER 21 n 21 SER 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 ALA 30 n 30 ALA 30 A VAL 31 n 31 VAL 31 A VAL 32 n 32 VAL 32 A THR 33 n 33 THR 33 A ILE 34 n 34 ILE 34 A GLU 35 n 35 GLU 35 A GLY 36 n 36 GLY 36 A ILE 37 n 37 ILE 37 A ILE 38 n 38 ILE 38 A LYS 39 n 39 LYS 39 A ILE 40 n 40 ILE 40 A ARG 41 n 41 ARG 41 A THR 42 n 42 THR 42 A GLY 43 n 43 GLY 43 A ASN 44 n 44 ASN 44 A LEU 45 n 45 LEU 45 A ASN 46 n 46 ASN 46 A GLN 47 n 47 GLN 47 A TYR 48 n 48 TYR 48 A SER 49 n 49 SER 49 A GLU 50 n 50 GLU 50 A GLN 51 n 51 GLN 51 A GLU 52 n 52 GLU 52 A LEU 53 n 53 LEU 53 A LEU 54 n 54 LEU 54 A ASP 55 n 55 ASP 55 A CYS 56 n 56 CYS 56 A ASP 57 n 57 ASP 57 A ARG 58 n 58 ARG 58 A ARG 59 n 59 ARG 59 A SER 60 n 60 SER 60 A TYR 61 n 61 TYR 61 A GLY 62 n 62 GLY 62 A CYS 63 n 63 CYS 63 A ASN 64 n 64 ASN 64 A GLY 65 n 65 GLY 65 A GLY 66 n 66 GLY 66 A TYR 67 n 67 TYR 67 A PRO 68 n 68 PRO 68 A TRP 69 n 69 TRP 69 A SER 70 n 70 SER 70 A ALA 71 n 71 ALA 71 A LEU 72 n 72 LEU 72 A GLN 73 n 73 GLN 73 A LEU 74 n 74 LEU 74 A VAL 75 n 75 VAL 75 A ALA 76 n 76 ALA 76 A GLN 77 n 77 GLN 77 A TYR 78 n 78 TYR 78 A GLY 79 n 79 GLY 79 A ILE 80 n 80 ILE 80 A HIS 81 n 81 HIS 81 A TYR 82 n 82 TYR 82 A ARG 83 n 83 ARG 83 A ASN 84 n 84 ASN 84 A THR 85 n 85 THR 85 A TYR 86 n 86 TYR 86 A PRO 87 n 87 PRO 87 A TYR 88 n 88 TYR 88 A GLU 89 n 89 GLU 89 A GLY 90 n 90 GLY 90 A VAL 91 n 91 VAL 91 A GLN 92 n 92 GLN 92 A ARG 93 n 93 ARG 93 A TYR 94 n 94 TYR 94 A CYS 95 n 95 CYS 95 A ARG 96 n 96 ARG 96 A SER 97 n 97 SER 97 A ARG 98 n 98 ARG 98 A GLU 99 n 99 GLU 99 A LYS 100 n 100 LYS 100 A GLY 101 n 101 GLY 101 A PRO 102 n 102 PRO 102 A TYR 103 n 103 TYR 103 A ALA 104 n 104 ALA 104 A ALA 105 n 105 ALA 105 A LYS 106 n 106 LYS 106 A THR 107 n 107 THR 107 A ASP 108 n 108 ASP 108 A GLY 109 n 109 GLY 109 A VAL 110 n 110 VAL 110 A ARG 111 n 111 ARG 111 A GLN 112 n 112 GLN 112 A VAL 113 n 113 VAL 113 A GLN 114 n 114 GLN 114 A PRO 115 n 115 PRO 115 A TYR 116 n 116 TYR 116 A ASN 117 n 117 ASN 117 A GLN 118 n 118 GLN 118 A GLY 119 n 119 GLY 119 A ALA 120 n 120 ALA 120 A LEU 121 n 121 LEU 121 A LEU 122 n 122 LEU 122 A TYR 123 n 123 TYR 123 A SER 124 n 124 SER 124 A ILE 125 n 125 ILE 125 A ALA 126 n 126 ALA 126 A ASN 127 n 127 ASN 127 A GLN 128 n 128 GLN 128 A PRO 129 n 129 PRO 129 A VAL 130 n 130 VAL 130 A SER 131 n 131 SER 131 A VAL 132 n 132 VAL 132 A VAL 133 n 133 VAL 133 A LEU 134 n 134 LEU 134 A GLN 135 n 135 GLN 135 A ALA 136 n 136 ALA 136 A ALA 137 n 137 ALA 137 A GLY 138 n 138 GLY 138 A LYS 139 n 139 LYS 139 A ASP 140 n 140 ASP 140 A PHE 141 n 141 PHE 141 A GLN 142 n 142 GLN 142 A LEU 143 n 143 LEU 143 A TYR 144 n 144 TYR 144 A ARG 145 n 145 ARG 145 A GLY 146 n 146 GLY 146 A GLY 147 n 147 GLY 147 A ILE 148 n 148 ILE 148 A PHE 149 n 149 PHE 149 A VAL 150 n 150 VAL 150 A GLY 151 n 151 GLY 151 A PRO 152 n 152 PRO 152 A CYS 153 n 153 CYS 153 A GLY 154 n 154 GLY 154 A ASN 155 n 155 ASN 155 A LYS 156 n 156 LYS 156 A VAL 157 n 157 VAL 157 A ASP 158 n 158 ASP 158 A HIS 159 n 159 HIS 159 A ALA 160 n 160 ALA 160 A VAL 161 n 161 VAL 161 A ALA 162 n 162 ALA 162 A ALA 163 n 163 ALA 163 A VAL 164 n 164 VAL 164 A GLY 165 n 165 GLY 165 A TYR 166 n 166 TYR 166 A GLY 167 n 167 GLY 167 A PRO 168 n 168 PRO 168 A ASN 169 n 169 ASN 169 A TYR 170 n 170 TYR 170 A ILE 171 n 171 ILE 171 A LEU 172 n 172 LEU 172 A ILE 173 n 173 ILE 173 A LYS 174 n 174 LYS 174 A ASN 175 n 175 ASN 175 A SER 176 n 176 SER 176 A TRP 177 n 177 TRP 177 A GLY 178 n 178 GLY 178 A THR 179 n 179 THR 179 A GLY 180 n 180 GLY 180 A TRP 181 n 181 TRP 181 A GLY 182 n 182 GLY 182 A GLU 183 n 183 GLU 183 A ASN 184 n 184 ASN 184 A GLY 185 n 185 GLY 185 A TYR 186 n 186 TYR 186 A ILE 187 n 187 ILE 187 A ARG 188 n 188 ARG 188 A ILE 189 n 189 ILE 189 A LYS 190 n 190 LYS 190 A ARG 191 n 191 ARG 191 A GLY 192 n 192 GLY 192 A THR 193 n 193 THR 193 A GLY 194 n 194 GLY 194 A ASN 195 n 195 ASN 195 A SER 196 n 196 SER 196 A TYR 197 n 197 TYR 197 A GLY 198 n 198 GLY 198 A VAL 199 n 199 VAL 199 A CYS 200 n 200 CYS 200 A GLY 201 n 201 GLY 201 A LEU 202 n 202 LEU 202 A TYR 203 n 203 TYR 203 A THR 204 n 204 THR 204 A SER 205 n 205 SER 205 A SER 206 n 206 SER 206 A PHE 207 n 207 PHE 207 A TYR 208 n 208 TYR 208 A PRO 209 n 209 PRO 209 A VAL 210 n 210 VAL 210 A LYS 211 n 211 LYS 211 A ASN 212 n 212 ASN 212 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 GLY 109 A O GLY 109 A N VAL 210 A N VAL 210 A O VAL 130 A O VAL 130 A N ALA 163 A N ALA 163 A O ALA 162 A O ALA 162 A N LYS 174 A N LYS 174 A O ILE 171 A O ILE 171 A N ILE 189 A N ILE 189 1 A CG ARG 59 A CG ARG 59 0 Y 1 A CD ARG 59 A CD ARG 59 0 Y 1 A NE ARG 59 A NE ARG 59 0 Y 1 A CZ ARG 59 A CZ ARG 59 0 Y 1 A NH1 ARG 59 A NH1 ARG 59 0 Y 1 A NH2 ARG 59 A NH2 ARG 59 0 Y 1 A CD GLN 73 A CD GLN 73 0 Y 1 A OE1 GLN 73 A OE1 GLN 73 0 Y 1 A NE2 GLN 73 A NE2 GLN 73 0 Y 1 A CG GLN 77 A CG GLN 77 0 Y 1 A CD GLN 77 A CD GLN 77 0 Y 1 A OE1 GLN 77 A OE1 GLN 77 0 Y 1 A NE2 GLN 77 A NE2 GLN 77 0 Y 1 A CD ARG 98 A CD ARG 98 0 Y 1 A NE ARG 98 A NE ARG 98 0 Y 1 A CZ ARG 98 A CZ ARG 98 0 Y 1 A NH1 ARG 98 A NH1 ARG 98 0 Y 1 A NH2 ARG 98 A NH2 ARG 98 0 Y 1 A CD ARG 145 A CD ARG 145 0 Y 1 A NE ARG 145 A NE ARG 145 0 Y 1 A CZ ARG 145 A CZ ARG 145 0 Y 1 A NH1 ARG 145 A NH1 ARG 145 0 Y 1 A NH2 ARG 145 A NH2 ARG 145 0 Y 1 A ARG 59 0.265 SIDE CHAIN 1 3.74 0.50 120.30 124.04 A A A NE CZ NH2 ARG ARG ARG 59 59 59 N 1 3.61 0.50 120.30 123.91 A A A NE CZ NH2 ARG ARG ARG 93 93 93 N 1 3.63 0.50 120.30 123.93 A A A NE CZ NH2 ARG ARG ARG 98 98 98 N 1 3.66 0.50 120.30 123.96 A A A NE CZ NH2 ARG ARG ARG 145 145 145 N 1 A PRO 15 -47.43 157.38 1 A ASN 64 -115.23 57.41 1 A VAL 75 -66.25 6.36 1 A GLN 77 -71.46 -77.07 1 A TYR 78 -75.83 -84.12 1 A PRO 87 -47.77 159.83 1 A CYS 95 -64.26 78.28 1 A ARG 96 -75.85 35.47 1 A SER 97 -62.21 -81.35 1 A GLU 99 -62.44 0.24 1 A TYR 144 -48.74 162.01 1 A ARG 145 -169.76 25.58 1 A ASP 158 -134.08 -69.30 1 A SER 176 -105.02 57.76 1 A CYS 200 59.06 -0.87 1 A LEU 202 -40.19 -11.41 1 A SER 205 -162.84 117.48 PARHCSDX.PRO TOPHCSDX.PR 26.4 DISORDERED SIDE-CHAINS HAVE THEIR OCCUPANCIES SET TO ZERO IN THE ENTRY, RESIDUES 59, 73, 77, 98, 145 0.306 0.217 0.217 2.5 10.0 1174 11372 8.3 80.0 RANDOM 100000 0.1 1 GROUP RESTRAINED THROUGHOUT 2.0 MOLECULAR REPLACEMENT PDB ENTRY 1PIP 2.5 10.0 42 1705 30 0 1633 0.011 1.595 24.85 1.441 0.31 0.283 2.61 47 649 8 6.2 53.0 2.5 10. 1BQI 11412 2.0 0.137 1 5.9 3.6 91 0.37 2.54 2.64 1.5 2.9 91 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 USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S'-SUBSITES. 1 N N 2 N N 3 N N A TRP 7 A TRP 7 HELX_P A LYS 10 A LYS 10 5 1 4 A CYS 25 A CYS 25 HELX_P A ARG 41 A ARG 41 1 2 17 A GLU 50 A GLU 50 HELX_P A CYS 56 A CYS 56 1 3 7 A PRO 68 A PRO 68 HELX_P A GLN 77 A GLN 77 1 4 10 A ARG 98 A ARG 98 HELX_P A LYS 100 A LYS 100 5 5 3 A ALA 120 A ALA 120 HELX_P A ILE 125 A ILE 125 1 6 6 A LYS 139 A LYS 139 HELX_P A LEU 143 A LEU 143 1 7 5 A VAL 199 A VAL 199 HELX_P A GLY 201 A GLY 201 5 8 3 disulf 2.036 A CYS 22 A SG CYS 22 1_555 A CYS 63 A SG CYS 63 1_555 disulf 2.049 A CYS 56 A SG CYS 56 1_555 A CYS 95 A SG CYS 95 1_555 disulf 2.032 A CYS 153 A SG CYS 153 1_555 A CYS 200 A SG CYS 200 1_555 HYDROLASE HYDROLASE, SULFHYDRYL PROTEINASE, PAPAIN A GLY 151 A GLY 151 1 A PRO 152 A PRO 152 -0.48 PAPA1_CARPA UNP 1 1 P00784 MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYID ETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWA FSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKT DGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYI RIKRGTGNSYGVCGLYTSSFYPVKN 134 345 1BQI 1 212 P00784 A 1 1 212 1 GLU conflict GLN 47 1BQI A P00784 UNP 180 47 1 GLU conflict GLN 118 1BQI A P00784 UNP 251 118 1 GLU conflict GLN 135 1BQI A P00784 UNP 268 135 2 4 anti-parallel anti-parallel anti-parallel anti-parallel A GLY 109 A GLY 109 A VAL 113 A VAL 113 A SER 206 A SER 206 A VAL 210 A VAL 210 A VAL 130 A VAL 130 A VAL 133 A VAL 133 A ALA 160 A ALA 160 A GLY 167 A GLY 167 A TYR 170 A TYR 170 A LYS 174 A LYS 174 A TYR 186 A TYR 186 A LYS 190 A LYS 190 CATALYTIC TRIAD Author 3 BINDING SITE FOR RESIDUE SBA A 300 A SBA 300 Software 5 A CYS 25 A CYS 25 3 1_555 A HIS 159 A HIS 159 3 1_555 A ASN 175 A ASN 175 3 1_555 A GLN 142 A GLN 142 5 1_555 A TRP 177 A TRP 177 5 1_555 A GLY 180 A GLY 180 5 1_555 A TRP 181 A TRP 181 5 1_555 A HOH 511 C HOH 5 1_555 5 C 1 2 1