0.023207 0.000000 0.000000 0.000000 0.009775 0.000000 0.000000 0.000000 0.020125 0.00000 0.00000 0.00000 CIS PROLINE - PRO A 152 Yamamoto, A. Tomoo, K. Doi, M. Ohishi, H. Inoue, M. Ishida, T. Yamamoto, D. Tsuboi, S. Okamoto, H. Okada, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 43.090 102.300 49.690 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 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 C6 H6 N2 O2 138.124 4-NITROANILINE PARANITROANILINE non-polymer 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 H6 O4 118.088 SUCCINIC ACID non-polymer 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 Biochemistry BICHAW 0033 0006-2960 31 11305 11309 10.1021/bi00161a007 1445868 Crystal structure of papain-succinyl-Gln-Val-Val-Ala-Ala-p-nitroanilide complex at 1.7-A resolution: noncovalent binding mode of a common sequence of endogenous thiol protease inhibitors. 1992 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 x-ray 1 1.0 23449.346 PAPAIN 3.4.22.2 1 man polymer 706.743 SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE 1 syn polymer no no IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN A polypeptide(L) no yes (SIN)QVVAA(NIT) XQVVAAX B 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 n n n n papaya Carica sample 3649 Carica papaya 2.27 45.72 pdbx_database_status struct_conf struct_conf_type repository Initial release Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Version format compliance Other Derived calculations Other 1 0 1993-10-31 1 1 2008-03-24 1 2 2011-07-13 1 3 2012-12-12 1 4 2017-11-29 _pdbx_database_status.process_site Y BNL 1992-10-03 REL SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PAPA_CARPA SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLU 47 GLN A 47 GLU 118 GLN A 118 GLU 135 GLN A 135 Inhibitor SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE Peptide-like 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 SIN 213 n 1 SIN 213 B GLN 214 n 2 GLN 400 B VAL 215 n 3 VAL 401 B VAL 216 n 4 VAL 402 B ALA 217 n 5 ALA 403 B ALA 218 n 6 ALA 404 B NIT 219 n 7 NIT 219 B author_defined_assembly 2 dimeric 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 VAL 5 A O VAL 5 A N TYR 166 A N TYR 166 A O HIS 159 A O HIS 159 A N LEU 134 A N LEU 134 A O SER 131 A O SER 131 A N PHE 207 A N PHE 207 A O SER 206 A O SER 206 A N VAL 113 A N VAL 113 A O GLY 109 A O GLY 109 A N LEU 172 A N LEU 172 A O ILE 171 A O ILE 171 A N ILE 189 A N ILE 189 1 6.05 0.80 106.30 112.35 A A A CD1 CG CD2 TRP TRP TRP 7 7 7 N 1 -5.47 0.80 107.30 101.83 A A A CE2 CD2 CG TRP TRP TRP 7 7 7 N 1 -3.20 0.50 120.30 117.10 A A A NE CZ NH2 ARG ARG ARG 8 8 8 N 1 4.83 0.80 106.30 111.13 A A A CD1 CG CD2 TRP TRP TRP 26 26 26 N 1 -9.61 1.60 122.70 113.09 A A A O C N CYS CYS ASN 63 63 64 Y 1 14.65 2.20 113.40 128.05 A A A CA CB CG ASN ASN ASN 64 64 64 N 1 6.66 0.80 106.30 112.96 A A A CD1 CG CD2 TRP TRP TRP 69 69 69 N 1 -5.51 0.80 107.30 101.79 A A A CE2 CD2 CG TRP TRP TRP 69 69 69 N 1 12.65 1.90 113.40 126.05 A A A CA CB CG TYR TYR TYR 94 94 94 N 1 4.48 0.50 120.30 124.78 A A A NE CZ NH1 ARG ARG ARG 98 98 98 N 1 -3.40 0.50 120.30 116.90 A A A NE CZ NH2 ARG ARG ARG 98 98 98 N 1 -3.73 0.50 120.30 116.57 A A A NE CZ NH2 ARG ARG ARG 111 111 111 N 1 -4.25 0.60 121.00 116.75 A A A CB CG CD2 TYR TYR TYR 116 116 116 N 1 -13.37 2.20 111.50 98.13 A A A N CA CB VAL VAL VAL 132 132 132 N 1 3.39 0.50 120.30 123.69 A A A NE CZ NH1 ARG ARG ARG 145 145 145 N 1 10.07 1.60 110.90 120.97 A A A CG1 CB CG2 VAL VAL VAL 161 161 161 N 1 5.28 0.80 106.30 111.58 A A A CD1 CG CD2 TRP TRP TRP 177 177 177 N 1 -4.96 0.80 107.30 102.34 A A A CE2 CD2 CG TRP TRP TRP 177 177 177 N 1 13.61 2.00 116.20 129.81 A A A CA C N TRP TRP GLY 177 177 178 Y 1 -11.38 1.70 123.20 111.82 A A A O C N TRP TRP GLY 177 177 178 Y 1 5.51 0.80 106.30 111.81 A A A CD1 CG CD2 TRP TRP TRP 181 181 181 N 1 -12.30 1.50 110.90 98.60 B B B CA CB CG2 VAL VAL VAL 401 401 401 N 1 17.33 2.70 111.00 128.33 B B B N CA C ALA ALA ALA 403 403 403 N 1 A A NE2 CD2 HIS HIS 81 81 -0.071 0.011 1.373 1.302 N 1 A A NE2 CD2 HIS HIS 159 159 -0.072 0.011 1.373 1.301 N 1 A B CG C1 GLN SIN 73 213 2.06 1_555 2_765 1 A ASN 64 49.93 21.04 1 A TYR 78 -121.02 -73.69 1 A TRP 177 -105.00 -160.91 1 B VAL 401 108.56 126.32 1 B ALA 403 -33.78 69.26 0.196 0.196 1.7 10.0 1 3.0 1.7 10.0 0 1705 0 0 1705 model building X-PLOR refinement X-PLOR phasing X-PLOR PAPAIN (E.C.3.4.22.2) COMPLEX WITH SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS 1 N N 2 N N A SER 24 A SER 24 HELX_P INCLUDING 3/10 REGION A THR 42 A THR 42 1 L1 19 A GLU 50 A GLU 50 HELX_P A ASP 57 A ASP 57 1 L2 8 A TYR 67 A TYR 67 HELX_P INCLUDING 3/10 REGION A TYR 78 A TYR 78 1 L3 12 A ASN 117 A ASN 117 HELX_P INCLUDING 3/10 REGION A ASN 127 A ASN 127 1 R1 11 A GLY 138 A GLY 138 HELX_P INCLUDING 3/10 REGION A GLN 142 A GLN 142 1 R2 5 disulf 2.021 A CYS 22 A SG CYS 22 1_555 A CYS 63 A SG CYS 63 1_555 disulf 2.044 A CYS 56 A SG CYS 56 1_555 A CYS 95 A SG CYS 95 1_555 disulf 2.023 A CYS 153 A SG CYS 153 1_555 A CYS 200 A SG CYS 200 1_555 covale 1.261 B SIN 213 B O2 SIN 1 1_555 A GLN 73 A CG GLN 73 2_764 covale 1.356 B SIN 213 B C4 SIN 1 1_555 B GLN 400 B N GLN 2 1_555 covale 1.417 B ALA 404 B C ALA 6 1_555 B NIT 219 B N1 NIT 7 1_555 HYDROLASE/HYDROLASE INHIBITOR THIOL PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX A GLY 151 A GLY 151 1 A PRO 152 A PRO 152 -2.12 PAPA1_CARPA UNP 1 134 P00784 1PIP PDB 2 1PIP 134 345 1PIP 1 212 P00784 A 1 1 212 213 219 1PIP 213 219 1PIP B 2 1 7 1 GLU CONFLICT GLN 47 1PIP A P00784 UNP 180 47 1 GLU CONFLICT GLN 118 1PIP A P00784 UNP 251 118 1 GLU CONFLICT GLN 135 1PIP A P00784 UNP 268 135 7 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A VAL 5 A VAL 5 A TRP 7 A TRP 7 A ASP 158 A ASP 158 A GLY 167 A GLY 167 A VAL 130 A VAL 130 A LEU 134 A LEU 134 A SER 206 A SER 206 A VAL 210 A VAL 210 A ASP 108 A ASP 108 A VAL 113 A VAL 113 A TYR 170 A TYR 170 A ASN 175 A ASN 175 A GLY 185 A GLY 185 A ARG 191 A ARG 191 BINDING SITE FOR CHAIN B OF SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE Software 8 A GLN 73 A GLN 73 8 2_764 A VAL 110 A VAL 110 8 2_764 A ALA 136 A ALA 136 8 1_555 A ALA 137 A ALA 137 8 1_555 A GLN 142 A GLN 142 8 1_555 A LYS 156 A LYS 156 8 1_555 A ASP 158 A ASP 158 8 1_555 A TRP 177 A TRP 177 8 1_555 19 P 21 21 21