0.011013 0.000000 0.000000 0.000000 0.011013 0.000000 0.000000 0.000000 0.007547 0.00000 0.00000 0.00000 CIS PROLINE - PRO H 37 LEU I 10 - GLN I 11 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION RESIDUE ASN H 60G IS GLYCOSYLATED. THE SUGAR ELECTRON DENSITY IS WEAK AND NO COORDINATES ARE PRESENT FOR THE SUGAR. Banner, D.W. Hadvary, P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 90.800 90.800 132.500 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 C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C27 H31 N5 O4 S 521.631 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine NAPAP peptide-like 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 J.Biol.Chem. JBCHA3 0071 0021-9258 266 20085 20093 1939071 Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors. 1991 IX Eur.J.Biochem. EJBCAI 0262 0014-2956 193 175 182 2226434 Geometry of binding of the benzamidine- and arginine-based inhibitors N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-pipe ridine (NAPAP) and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) to human alpha-thrombin. X-ray crystallographic determination of the NAPAP-trypsin complex and modeling of NAPAP-thrombin and MQPA-thrombin. 1990 UK Embo J. EMJODG 0897 0261-4189 8 3467 3475 2583108 The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. 1989 US Protein Sci. PRCIEI 0795 0961-8368 1 426 471 1304349 The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships. 1992 US Science SCIEAS 0038 0036-8075 249 277 280 2374926 The structure of a complex of recombinant hirudin and human alpha-thrombin. 1990 IX Eur.J.Biochem. EJBCAI 0262 0014-2956 206 187 195 1587268 The interaction of thrombin with fibrinogen. A structural basis for its specificity. 1992 UK Embo J. EMJODG 0897 0261-4189 9 2361 2365 2369893 Crystal structure of the thrombin-hirudin complex: a novel mode of serine protease inhibition. 1990 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 4096.534 ALPHA-THROMBIN (SMALL SUBUNIT) 3.4.21.5 1 man polymer 29780.219 ALPHA-THROMBIN (LARGE SUBUNIT) 3.4.21.5 1 man polymer 1411.465 HIRUDIN IIIA 1 man polymer 521.631 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine 1 syn non-polymer 18.015 water 50 nat water no no TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR L polypeptide(L) no no IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE H polypeptide(L) no no DFEEIPEEYLQ DFEEIPEEYLQ I 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n 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 sample 9606 PLASMA Homo sapiens human Homo sample 9606 PLASMA Homo sapiens medicinal leech Hirudo sample 6421 Hirudo medicinalis 3.87 68.20 repository Initial release Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Version format compliance Other 1 0 1994-01-31 1 1 2008-03-03 1 2 2011-07-13 1 3 2012-12-12 Y 1992-08-19 REL MID 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine HOH water THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *I* IS USED FOR A C-TERMINAL HIRUDIN PEPTIDE ((DES-AMINO ASP55)HIRUDIN(55-65)). THE RESIDUES OF CHAIN I ARE NUMBERED FROM 1 - 11. IT BINDS IN THE ANION-BINDING EXOSITE. NAPAP IS N==ALPHA==-(2-NAPHTHYL-SULFONYL-GLYCYL)-(DL)- PARA-AMIDINOPHENYLALANYL-PIPERIDINE (STUERZEBECHER ET AL., THROMB. RES. VOL 29 PP 635-642 (1983)). THE AUTHORS SHOW HERE THAT THE D-ISOMER BINDS TO THROMBIN. Inhibitor N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide Peptide-like MID 1 4 MID MID 1 H HOH 31 5 HOH HOH 30 L HOH 49 5 HOH HOH 45 L HOH 53 5 HOH HOH 48 L HOH 63 5 HOH HOH 63 L HOH 18 5 HOH HOH 248 H HOH 20 5 HOH HOH 249 H HOH 21 5 HOH HOH 250 H HOH 23 5 HOH HOH 251 H HOH 24 5 HOH HOH 252 H HOH 25 5 HOH HOH 253 H HOH 26 5 HOH HOH 254 H HOH 27 5 HOH HOH 255 H HOH 28 5 HOH HOH 256 H HOH 30 5 HOH HOH 257 H HOH 32 5 HOH HOH 258 H HOH 33 5 HOH HOH 259 H HOH 34 5 HOH HOH 260 H HOH 35 5 HOH HOH 261 H HOH 36 5 HOH HOH 262 H HOH 37 5 HOH HOH 263 H HOH 39 5 HOH HOH 264 H HOH 41 5 HOH HOH 265 H HOH 42 5 HOH HOH 266 H HOH 43 5 HOH HOH 267 H HOH 44 5 HOH HOH 268 H HOH 46 5 HOH HOH 269 H HOH 47 5 HOH HOH 270 H HOH 48 5 HOH HOH 271 H HOH 50 5 HOH HOH 272 H HOH 52 5 HOH HOH 273 H HOH 54 5 HOH HOH 274 H HOH 55 5 HOH HOH 275 H HOH 56 5 HOH HOH 276 H HOH 57 5 HOH HOH 277 H HOH 60 5 HOH HOH 278 H HOH 48 5 HOH HOH 279 H HOH 49 5 HOH HOH 280 H HOH 50 5 HOH HOH 281 H HOH 51 5 HOH HOH 282 H HOH 53 5 HOH HOH 283 H HOH 54 5 HOH HOH 284 H HOH 55 5 HOH HOH 285 H HOH 61 5 HOH HOH 286 H HOH 62 5 HOH HOH 287 H HOH 64 5 HOH HOH 288 H HOH 65 5 HOH HOH 289 H HOH 16 5 HOH HOH 16 I HOH 17 5 HOH HOH 17 I HOH 19 5 HOH HOH 19 I HOH 22 5 HOH HOH 22 I n 1 H 1 L n 2 G 1 L n 3 F 1 L n 4 E 1 L n 5 D 1 L GLU 1 n 6 C GLU 1 L ALA 1 n 7 B ALA 1 L ASP 1 n 8 A ASP 1 L CYS 1 n 9 CYS 1 L GLY 2 n 10 GLY 2 L LEU 3 n 11 LEU 3 L ARG 4 n 12 ARG 4 L PRO 5 n 13 PRO 5 L LEU 6 n 14 LEU 6 L PHE 7 n 15 PHE 7 L GLU 8 n 16 GLU 8 L LYS 9 n 17 LYS 9 L LYS 10 n 18 LYS 10 L SER 11 n 19 SER 11 L LEU 12 n 20 LEU 12 L GLU 13 n 21 GLU 13 L ASP 14 n 22 ASP 14 L LYS 14 n 23 A LYS 14 L THR 14 n 24 B THR 14 L GLU 14 n 25 C GLU 14 L ARG 14 n 26 D ARG 14 L GLU 14 n 27 E GLU 14 L LEU 14 n 28 F LEU 14 L LEU 14 n 29 G LEU 14 L GLU 14 n 30 H GLU 14 L SER 14 n 31 I SER 14 L TYR 14 n 32 J TYR 14 L ILE 14 n 33 K ILE 14 L ASP 14 n 34 L ASP 14 L n 35 M 14 L n 36 N 14 L ILE 16 n 1 ILE 16 H VAL 17 n 2 VAL 17 H GLU 18 n 3 GLU 18 H GLY 19 n 4 GLY 19 H SER 20 n 5 SER 20 H ASP 21 n 6 ASP 21 H ALA 22 n 7 ALA 22 H GLU 23 n 8 GLU 23 H ILE 24 n 9 ILE 24 H GLY 25 n 10 GLY 25 H MET 26 n 11 MET 26 H SER 27 n 12 SER 27 H PRO 28 n 13 PRO 28 H TRP 29 n 14 TRP 29 H GLN 30 n 15 GLN 30 H VAL 31 n 16 VAL 31 H MET 32 n 17 MET 32 H LEU 33 n 18 LEU 33 H PHE 34 n 19 PHE 34 H ARG 35 n 20 ARG 35 H LYS 36 n 21 LYS 36 H SER 36 n 22 A SER 36 H PRO 37 n 23 PRO 37 H GLN 38 n 24 GLN 38 H GLU 39 n 25 GLU 39 H LEU 40 n 26 LEU 40 H LEU 41 n 27 LEU 41 H CYS 42 n 28 CYS 42 H GLY 43 n 29 GLY 43 H ALA 44 n 30 ALA 44 H SER 45 n 31 SER 45 H LEU 46 n 32 LEU 46 H ILE 47 n 33 ILE 47 H SER 48 n 34 SER 48 H ASP 49 n 35 ASP 49 H ARG 50 n 36 ARG 50 H TRP 51 n 37 TRP 51 H VAL 52 n 38 VAL 52 H LEU 53 n 39 LEU 53 H THR 54 n 40 THR 54 H ALA 55 n 41 ALA 55 H ALA 56 n 42 ALA 56 H HIS 57 n 43 HIS 57 H CYS 58 n 44 CYS 58 H LEU 59 n 45 LEU 59 H LEU 60 n 46 LEU 60 H TYR 60 n 47 A TYR 60 H PRO 60 n 48 B PRO 60 H PRO 60 n 49 C PRO 60 H TRP 60 n 50 D TRP 60 H ASP 60 n 51 E ASP 60 H LYS 60 n 52 F LYS 60 H ASN 60 n 53 G ASN 60 H PHE 60 n 54 H PHE 60 H THR 60 n 55 I THR 60 H GLU 61 n 56 GLU 61 H ASN 62 n 57 ASN 62 H ASP 63 n 58 ASP 63 H LEU 64 n 59 LEU 64 H LEU 65 n 60 LEU 65 H VAL 66 n 61 VAL 66 H ARG 67 n 62 ARG 67 H ILE 68 n 63 ILE 68 H GLY 69 n 64 GLY 69 H LYS 70 n 65 LYS 70 H HIS 71 n 66 HIS 71 H SER 72 n 67 SER 72 H ARG 73 n 68 ARG 73 H THR 74 n 69 THR 74 H ARG 75 n 70 ARG 75 H TYR 76 n 71 TYR 76 H GLU 77 n 72 GLU 77 H ARG 77 n 73 A ARG 77 H ASN 78 n 74 ASN 78 H ILE 79 n 75 ILE 79 H GLU 80 n 76 GLU 80 H LYS 81 n 77 LYS 81 H ILE 82 n 78 ILE 82 H SER 83 n 79 SER 83 H MET 84 n 80 MET 84 H LEU 85 n 81 LEU 85 H GLU 86 n 82 GLU 86 H LYS 87 n 83 LYS 87 H ILE 88 n 84 ILE 88 H TYR 89 n 85 TYR 89 H ILE 90 n 86 ILE 90 H HIS 91 n 87 HIS 91 H PRO 92 n 88 PRO 92 H ARG 93 n 89 ARG 93 H TYR 94 n 90 TYR 94 H ASN 95 n 91 ASN 95 H TRP 96 n 92 TRP 96 H ARG 97 n 93 ARG 97 H GLU 97 n 94 A GLU 97 H ASN 98 n 95 ASN 98 H LEU 99 n 96 LEU 99 H ASP 100 n 97 ASP 100 H ARG 101 n 98 ARG 101 H ASP 102 n 99 ASP 102 H ILE 103 n 100 ILE 103 H ALA 104 n 101 ALA 104 H LEU 105 n 102 LEU 105 H MET 106 n 103 MET 106 H LYS 107 n 104 LYS 107 H LEU 108 n 105 LEU 108 H LYS 109 n 106 LYS 109 H LYS 110 n 107 LYS 110 H PRO 111 n 108 PRO 111 H VAL 112 n 109 VAL 112 H ALA 113 n 110 ALA 113 H PHE 114 n 111 PHE 114 H SER 115 n 112 SER 115 H ASP 116 n 113 ASP 116 H TYR 117 n 114 TYR 117 H ILE 118 n 115 ILE 118 H HIS 119 n 116 HIS 119 H PRO 120 n 117 PRO 120 H VAL 121 n 118 VAL 121 H CYS 122 n 119 CYS 122 H LEU 123 n 120 LEU 123 H PRO 124 n 121 PRO 124 H ASP 125 n 122 ASP 125 H ARG 126 n 123 ARG 126 H GLU 127 n 124 GLU 127 H THR 128 n 125 THR 128 H ALA 129 n 126 ALA 129 H ALA 129 n 127 A ALA 129 H SER 129 n 128 B SER 129 H LEU 129 n 129 C LEU 129 H LEU 130 n 130 LEU 130 H GLN 131 n 131 GLN 131 H ALA 132 n 132 ALA 132 H GLY 133 n 133 GLY 133 H TYR 134 n 134 TYR 134 H LYS 135 n 135 LYS 135 H GLY 136 n 136 GLY 136 H ARG 137 n 137 ARG 137 H VAL 138 n 138 VAL 138 H THR 139 n 139 THR 139 H GLY 140 n 140 GLY 140 H TRP 141 n 141 TRP 141 H GLY 142 n 142 GLY 142 H ASN 143 n 143 ASN 143 H LEU 144 n 144 LEU 144 H LYS 145 n 145 LYS 145 H GLU 146 n 146 GLU 146 H THR 147 n 147 THR 147 H TRP 148 n 148 TRP 148 H THR 149 n 149 THR 149 H ALA 149 n 150 A ALA 149 H ASN 149 n 151 B ASN 149 H VAL 149 n 152 C VAL 149 H GLY 149 n 153 D GLY 149 H LYS 149 n 154 E LYS 149 H GLY 150 n 155 GLY 150 H GLN 151 n 156 GLN 151 H PRO 152 n 157 PRO 152 H SER 153 n 158 SER 153 H VAL 154 n 159 VAL 154 H LEU 155 n 160 LEU 155 H GLN 156 n 161 GLN 156 H VAL 157 n 162 VAL 157 H VAL 158 n 163 VAL 158 H ASN 159 n 164 ASN 159 H LEU 160 n 165 LEU 160 H PRO 161 n 166 PRO 161 H ILE 162 n 167 ILE 162 H VAL 163 n 168 VAL 163 H GLU 164 n 169 GLU 164 H ARG 165 n 170 ARG 165 H PRO 166 n 171 PRO 166 H VAL 167 n 172 VAL 167 H CYS 168 n 173 CYS 168 H LYS 169 n 174 LYS 169 H ASP 170 n 175 ASP 170 H SER 171 n 176 SER 171 H THR 172 n 177 THR 172 H ARG 173 n 178 ARG 173 H ILE 174 n 179 ILE 174 H ARG 175 n 180 ARG 175 H ILE 176 n 181 ILE 176 H THR 177 n 182 THR 177 H ASP 178 n 183 ASP 178 H ASN 179 n 184 ASN 179 H MET 180 n 185 MET 180 H PHE 181 n 186 PHE 181 H CYS 182 n 187 CYS 182 H ALA 183 n 188 ALA 183 H GLY 184 n 189 GLY 184 H TYR 184 n 190 A TYR 184 H LYS 185 n 191 LYS 185 H PRO 186 n 192 PRO 186 H ASP 186 n 193 A ASP 186 H GLU 186 n 194 B GLU 186 H GLY 186 n 195 C GLY 186 H LYS 186 n 196 D LYS 186 H ARG 187 n 197 ARG 187 H GLY 188 n 198 GLY 188 H ASP 189 n 199 ASP 189 H ALA 190 n 200 ALA 190 H CYS 191 n 201 CYS 191 H GLU 192 n 202 GLU 192 H GLY 193 n 203 GLY 193 H ASP 194 n 204 ASP 194 H SER 195 n 205 SER 195 H GLY 196 n 206 GLY 196 H GLY 197 n 207 GLY 197 H PRO 198 n 208 PRO 198 H PHE 199 n 209 PHE 199 H VAL 200 n 210 VAL 200 H MET 201 n 211 MET 201 H LYS 202 n 212 LYS 202 H SER 203 n 213 SER 203 H PRO 204 n 214 PRO 204 H PHE 204 n 215 A PHE 204 H ASN 204 n 216 B ASN 204 H ASN 205 n 217 ASN 205 H ARG 206 n 218 ARG 206 H TRP 207 n 219 TRP 207 H TYR 208 n 220 TYR 208 H GLN 209 n 221 GLN 209 H MET 210 n 222 MET 210 H GLY 211 n 223 GLY 211 H ILE 212 n 224 ILE 212 H VAL 213 n 225 VAL 213 H SER 214 n 226 SER 214 H TRP 215 n 227 TRP 215 H GLY 216 n 228 GLY 216 H GLU 217 n 229 GLU 217 H GLY 219 n 230 GLY 219 H CYS 220 n 231 CYS 220 H ASP 221 n 232 ASP 221 H ARG 221 n 233 A ARG 221 H ASP 222 n 234 ASP 222 H GLY 223 n 235 GLY 223 H LYS 224 n 236 LYS 224 H TYR 225 n 237 TYR 225 H GLY 226 n 238 GLY 226 H PHE 227 n 239 PHE 227 H TYR 228 n 240 TYR 228 H THR 229 n 241 THR 229 H HIS 230 n 242 HIS 230 H VAL 231 n 243 VAL 231 H PHE 232 n 244 PHE 232 H ARG 233 n 245 ARG 233 H LEU 234 n 246 LEU 234 H LYS 235 n 247 LYS 235 H LYS 236 n 248 LYS 236 H TRP 237 n 249 TRP 237 H ILE 238 n 250 ILE 238 H GLN 239 n 251 GLN 239 H LYS 240 n 252 LYS 240 H VAL 241 n 253 VAL 241 H ILE 242 n 254 ILE 242 H ASP 243 n 255 ASP 243 H GLN 244 n 256 GLN 244 H PHE 245 n 257 PHE 245 H GLY 246 n 258 GLY 246 H n 259 247 H ASP 1 n 1 ASP 1 I PHE 2 n 2 PHE 2 I GLU 3 n 3 GLU 3 I GLU 4 n 4 GLU 4 I ILE 5 n 5 ILE 5 I PRO 6 n 6 PRO 6 I GLU 7 n 7 GLU 7 I GLU 8 n 8 GLU 8 I TYR 9 n 9 TYR 9 I LEU 10 n 10 LEU 10 I GLN 11 n 11 GLN 11 I author_and_software_defined_assembly PISA 3 trimeric 4190 -18 13430 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 H O SER 20 B O SER 5 H N VAL 157 B N VAL 162 H O LEU 160 B O LEU 165 H N GLY 136 B N GLY 136 H N THR 139 B N THR 139 H O PRO 198 B O PRO 208 H O MET 201 B O MET 211 H N TYR 208 B N TYR 220 H O TRP 215 B O TRP 227 H N PHE 227 B N PHE 239 H N TYR 228 B N TYR 240 H O PHE 181 B O PHE 186 H N ARG 35 B N ARG 20 H O GLU 39 B O GLU 25 H N ILE 47 B N ILE 33 H O TRP 51 B O TRP 37 H N THR 54 B N THR 40 H O ALA 104 B O ALA 101 H O LYS 107 B O LYS 104 H N GLU 86 B N GLU 82 H N LEU 85 B N LEU 81 H O LEU 64 B O LEU 59 H O ARG 67 B O ARG 62 H N MET 32 B N MET 17 C 1 L CG GLU 1 A CG GLU 6 1 Y C 1 L CD GLU 1 A CD GLU 6 1 Y C 1 L OE1 GLU 1 A OE1 GLU 6 1 Y C 1 L OE2 GLU 1 A OE2 GLU 6 1 Y A 1 H CG ARG 77 B CG ARG 73 1 Y A 1 H CD ARG 77 B CD ARG 73 1 Y A 1 H NE ARG 77 B NE ARG 73 1 Y A 1 H CZ ARG 77 B CZ ARG 73 1 Y A 1 H NH1 ARG 77 B NH1 ARG 73 1 Y A 1 H NH2 ARG 77 B NH2 ARG 73 1 Y 1 H CG ASN 78 B CG ASN 74 1 Y 1 H OD1 ASN 78 B OD1 ASN 74 1 Y 1 H ND2 ASN 78 B ND2 ASN 74 1 Y 1 H CG LYS 81 B CG LYS 77 1 Y 1 H CD LYS 81 B CD LYS 77 1 Y 1 H CE LYS 81 B CE LYS 77 1 Y 1 H NZ LYS 81 B NZ LYS 77 1 Y 1 H CG ARG 93 B CG ARG 89 1 Y 1 H CD ARG 93 B CD ARG 89 1 Y 1 H NE ARG 93 B NE ARG 89 1 Y 1 H CZ ARG 93 B CZ ARG 89 1 Y 1 H NH1 ARG 93 B NH1 ARG 89 1 Y 1 H NH2 ARG 93 B NH2 ARG 89 1 Y 1 H CG ARG 97 B CG ARG 93 1 Y 1 H CD ARG 97 B CD ARG 93 1 Y 1 H NE ARG 97 B NE ARG 93 1 Y 1 H CZ ARG 97 B CZ ARG 93 1 Y 1 H NH1 ARG 97 B NH1 ARG 93 1 Y 1 H NH2 ARG 97 B NH2 ARG 93 1 Y 1 H CG GLU 127 B CG GLU 124 1 Y 1 H CD GLU 127 B CD GLU 124 1 Y 1 H OE1 GLU 127 B OE1 GLU 124 1 Y 1 H OE2 GLU 127 B OE2 GLU 124 1 Y E 1 H CG LYS 149 B CG LYS 154 1 Y E 1 H CD LYS 149 B CD LYS 154 1 Y E 1 H CE LYS 149 B CE LYS 154 1 Y E 1 H NZ LYS 149 B NZ LYS 154 1 Y 1 H CG LYS 169 B CG LYS 174 1 Y 1 H CD LYS 169 B CD LYS 174 1 Y 1 H CE LYS 169 B CE LYS 174 1 Y 1 H NZ LYS 169 B NZ LYS 174 1 Y 1 H CG ARG 173 B CG ARG 178 1 Y 1 H CD ARG 173 B CD ARG 178 1 Y 1 H NE ARG 173 B NE ARG 178 1 Y 1 H CZ ARG 173 B CZ ARG 178 1 Y 1 H NH1 ARG 173 B NH1 ARG 178 1 Y 1 H NH2 ARG 173 B NH2 ARG 178 1 Y 1 H CA GLY 246 B CA GLY 258 1 Y 1 H C GLY 246 B C GLY 258 1 Y 1 H O GLY 246 B O GLY 258 1 Y 1 I N ASP 1 C N ASP 1 1 Y 1 I CG GLU 8 C CG GLU 8 1 Y 1 I CD GLU 8 C CD GLU 8 1 Y 1 I OE1 GLU 8 C OE1 GLU 8 1 Y 1 I OE2 GLU 8 C OE2 GLU 8 1 Y 1 I CA GLN 11 C CA GLN 11 1 Y 1 I C GLN 11 C C GLN 11 1 Y 1 I O GLN 11 C O GLN 11 1 Y 1 I CB GLN 11 C CB GLN 11 1 Y 1 I CG GLN 11 C CG GLN 11 1 Y 1 I CD GLN 11 C CD GLN 11 1 Y 1 I OE1 GLN 11 C OE1 GLN 11 1 Y 1 I NE2 GLN 11 C NE2 GLN 11 1 Y H 1 L THR 1 A THR 1 1 Y G 1 L PHE 1 A PHE 2 1 Y F 1 L GLY 1 A GLY 3 1 Y E 1 L SER 1 A SER 4 1 Y D 1 L GLY 1 A GLY 5 1 Y M 1 L GLY 14 A GLY 35 1 Y N 1 L ARG 14 A ARG 36 1 Y 1 H GLU 247 B GLU 259 1 Y L L L 1 -6.86 0.90 118.30 111.44 L L L CB CG OD2 ASP ASP ASP 14 14 14 N 1 -5.81 0.90 118.30 112.49 H H H CB CG OD1 ASP ASP ASP 21 21 21 N 1 -6.41 0.90 118.30 111.89 H H H CB CG OD2 ASP ASP ASP 49 49 49 N E E E 1 5.46 0.90 118.30 123.76 H H H CB CG OD1 ASP ASP ASP 60 60 60 N E E E 1 -7.68 0.90 118.30 110.62 H H H CB CG OD2 ASP ASP ASP 60 60 60 N 1 5.83 0.90 118.30 124.13 H H H CB CG OD1 ASP ASP ASP 100 100 100 N 1 3.10 0.50 120.30 123.40 H H H NE CZ NH1 ARG ARG ARG 101 101 101 N 1 -3.12 0.50 120.30 117.18 H H H NE CZ NH2 ARG ARG ARG 101 101 101 N 1 -6.13 0.90 118.30 112.17 H H H CB CG OD2 ASP ASP ASP 102 102 102 N 1 -5.66 0.90 118.30 112.64 H H H CB CG OD2 ASP ASP ASP 116 116 116 N 1 -5.84 0.90 118.30 112.46 H H H CB CG OD1 ASP ASP ASP 125 125 125 N 1 5.65 0.90 118.30 123.95 H H H CB CG OD2 ASP ASP ASP 125 125 125 N 1 5.44 0.90 118.30 123.74 H H H CB CG OD1 ASP ASP ASP 170 170 170 N 1 -6.24 0.90 118.30 112.06 H H H CB CG OD2 ASP ASP ASP 170 170 170 N 1 -6.19 0.90 118.30 112.11 H H H CB CG OD2 ASP ASP ASP 178 178 178 N A A A 1 -5.81 0.90 118.30 112.49 H H H CB CG OD1 ASP ASP ASP 186 186 186 N 1 3.21 0.50 120.30 123.51 H H H NE CZ NH1 ARG ARG ARG 187 187 187 N 1 -7.46 0.90 118.30 110.84 H H H CB CG OD1 ASP ASP ASP 189 189 189 N 1 6.97 0.90 118.30 125.27 H H H CB CG OD2 ASP ASP ASP 189 189 189 N 1 -5.63 0.90 118.30 112.67 H H H CB CG OD2 ASP ASP ASP 243 243 243 N E E 1 L L CD OE1 GLU GLU 14 14 0.089 0.011 1.252 1.341 N 1 H H CD OE2 GLU GLU 18 18 0.083 0.011 1.252 1.335 N 1 H H CD OE2 GLU GLU 39 39 0.076 0.011 1.252 1.328 N 1 H H CD OE1 GLU GLU 61 61 0.068 0.011 1.252 1.320 N 1 H H CD OE2 GLU GLU 86 86 0.078 0.011 1.252 1.330 N A A 1 H H CD OE1 GLU GLU 97 97 0.076 0.011 1.252 1.328 N B B 1 H H CD OE2 GLU GLU 186 186 0.075 0.011 1.252 1.327 N 1 H H CD OE2 GLU GLU 192 192 0.084 0.011 1.252 1.336 N 1 I I CD OE2 GLU GLU 4 4 0.095 0.011 1.252 1.347 N 1 I I CD OE2 GLU GLU 7 7 0.072 0.011 1.252 1.324 N 1 L PHE 7 -125.25 -85.65 1 L SER 11 58.70 19.73 1 H SER 48 174.77 169.59 1 H ASP 49 -37.02 -29.10 1 H HIS 57 -50.80 -4.63 A 1 H TYR 60 -156.07 79.30 C 1 H PRO 60 -41.49 -4.69 G 1 H ASN 60 -160.70 79.10 1 H HIS 71 -122.57 -58.01 1 H SER 115 -154.96 -159.03 B 1 H ASN 149 58.50 -3.17 C 1 H VAL 149 -107.47 73.77 E 1 H LYS 149 -163.97 107.67 1 H SER 214 -109.31 -74.12 1 H GLN 244 -65.63 4.96 PROLINES ARE TOO FLAT AS A BAD DICTIONARY WAS USED. ASN H 60G IS GLYCOSYLATED. THE SUGAR ELECTRON DENSITY IS WEAK AND NO COORDINATES ARE PRESENT FOR THE SUGAR. 0.156 3.0 25.0 1 0.0 3.0 25.0 50 2445 37 0 2358 0.015 1.98 refinement TNT ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX WITH (DES-AMINO ASP 55) HIRUDIN (RESIDUES 55 - 65) AND NAPAP CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N L PHE 7 A PHE 15 HELX_P L SER 11 A SER 19 5 1 5 L THR 14 A THR 24 HELX_P L SER 14 A SER 31 1 2 8 B I H ALA 55 B ALA 41 HELX_P H CYS 58 B CYS 44 5 3 4 H PRO 60 B PRO 48 HELX_P H ASP 60 B ASP 51 5 4 4 B E H ASP 125 B ASP 122 HELX_P H LEU 130 B LEU 130 1 5 9 H GLU 164 B GLU 169 HELX_P H ASP 170 B ASP 175 1 6 7 H LYS 185 B LYS 191 HELX_P H GLY 186 B GLY 195 5 7 5 C H LEU 234 B LEU 246 HELX_P H ASP 243 B ASP 255 1 8 10 I PRO 6 C PRO 6 HELX_P I LEU 10 C LEU 10 5 9 5 disulf 2.023 L CYS 1 A SG CYS 9 1_555 H CYS 122 B SG CYS 119 1_555 disulf 2.061 H CYS 42 B SG CYS 28 1_555 H CYS 58 B SG CYS 44 1_555 disulf 2.028 H CYS 168 B SG CYS 173 1_555 H CYS 182 B SG CYS 187 1_555 disulf 1.950 H CYS 191 B SG CYS 201 1_555 H CYS 220 B SG CYS 231 1_555 HYDROLASE/HYROLASE INHIBITOR SERINE PROTEINASE, HYDROLASE-HYROLASE INHIBITOR COMPLEX H SER 36 B SER 22 A 1 H PRO 37 B PRO 23 -1.03 THRB_HUMAN UNP 1 328 P00734 THRB_HUMAN UNP 2 364 P00734 ITHH_HIRME UNP 3 55 P28508 328 363 1DWD 1 14 P00734 H N L 1 1 36 364 622 1DWD 16 247 P00734 H 2 1 259 55 65 1DWD 1 11 P28508 I 3 1 11 7 7 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel H SER 20 B SER 5 H ASP 21 B ASP 6 H GLN 156 B GLN 161 H PRO 161 B PRO 166 H LYS 135 B LYS 135 H GLY 140 B GLY 140 H PRO 198 B PRO 208 H LYS 202 B LYS 212 H TRP 207 B TRP 219 H TRP 215 B TRP 227 H GLY 226 B GLY 238 H HIS 230 B HIS 242 H MET 180 B MET 185 H ALA 183 B ALA 188 H GLN 30 B GLN 15 H ARG 35 B ARG 20 H GLU 39 B GLU 25 H SER 48 B SER 34 H TRP 51 B TRP 37 H THR 54 B THR 40 H ALA 104 B ALA 101 H LEU 108 B LEU 105 H LYS 81 B LYS 77 H ILE 90 B ILE 86 H LEU 64 B LEU 59 H ILE 68 B ILE 63 H GLN 30 B GLN 15 H ARG 35 B ARG 20 CATALYTIC SITE Author 3 BINDING SITE FOR RESIDUE MID H 1 Software 12 BINDING SITE FOR CHAIN I OF HIRUDIN IIIA Software 16 H HIS 57 B HIS 43 3 1_555 H ASP 102 B ASP 99 3 1_555 H SER 195 B SER 205 3 1_555 H HIS 57 B HIS 43 12 1_555 H ASN 98 B ASN 95 12 1_555 H LEU 99 B LEU 96 12 1_555 H ILE 174 B ILE 179 12 1_555 H ASP 189 B ASP 199 12 1_555 H ALA 190 B ALA 200 12 1_555 H SER 195 B SER 205 12 1_555 H TRP 215 B TRP 227 12 1_555 H GLY 216 B GLY 228 12 1_555 H GLY 219 B GLY 230 12 1_555 H HOH 264 F HOH 12 1_555 H HOH 270 F HOH 12 1_555 H LYS 36 B LYS 21 16 1_555 H GLN 38 B GLN 24 16 1_555 H ARG 73 B ARG 68 16 1_555 H THR 74 B THR 69 16 1_555 H ARG 75 B ARG 70 16 1_555 H ARG 75 B ARG 70 16 7_555 H TYR 76 B TYR 71 16 1_555 H ILE 82 B ILE 78 16 1_555 H MET 84 B MET 80 16 1_555 H LYS 236 B LYS 248 16 3_544 H GLN 239 B GLN 251 16 3_544 H HOH 282 F HOH 16 1_555 I HOH 16 G HOH 16 1_555 I HOH 17 G HOH 16 1_555 I HOH 19 G HOH 16 7_555 I HOH 22 G HOH 16 1_555 96 P 43 21 2