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 PHE H 245 - GLY H 246 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION LEU I 10 - GLN I 11 OMEGA =359.98 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 C7 H8 N2 120.152 BENZAMIDINE 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 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 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 syn polymer 120.152 BENZAMIDINE 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 sample 9606 PLASMA Homo sapiens human sample 9606 PLASMA Homo sapiens 3.87 68.20 repository Initial release Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Version format compliance 1 0 1994-01-31 1 1 2008-03-03 1 2 2011-07-13 Y 1992-08-19 REL BEN BENZAMIDINE HOH water 6421 medicinal leech Hirudo medicinalis sample 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. BEN 1 4 BEN BEN 1 H HOH 312 5 HOH HOH 312 L HOH 327 5 HOH HOH 327 L HOH 330 5 HOH HOH 330 L HOH 345 5 HOH HOH 345 L HOH 300 5 HOH HOH 300 H HOH 302 5 HOH HOH 302 H HOH 305 5 HOH HOH 305 H HOH 306 5 HOH HOH 306 H HOH 307 5 HOH HOH 307 H HOH 308 5 HOH HOH 308 H HOH 309 5 HOH HOH 309 H HOH 310 5 HOH HOH 310 H HOH 311 5 HOH HOH 311 H HOH 313 5 HOH HOH 313 H HOH 314 5 HOH HOH 314 H HOH 315 5 HOH HOH 315 H HOH 316 5 HOH HOH 316 H HOH 317 5 HOH HOH 317 H HOH 318 5 HOH HOH 318 H HOH 319 5 HOH HOH 319 H HOH 320 5 HOH HOH 320 H HOH 321 5 HOH HOH 321 H HOH 322 5 HOH HOH 322 H HOH 323 5 HOH HOH 323 H HOH 324 5 HOH HOH 324 H HOH 325 5 HOH HOH 325 H HOH 326 5 HOH HOH 326 H HOH 328 5 HOH HOH 328 H HOH 329 5 HOH HOH 329 H HOH 331 5 HOH HOH 331 H HOH 332 5 HOH HOH 332 H HOH 333 5 HOH HOH 333 H HOH 334 5 HOH HOH 334 H HOH 335 5 HOH HOH 335 H HOH 336 5 HOH HOH 336 H HOH 337 5 HOH HOH 337 H HOH 338 5 HOH HOH 338 H HOH 339 5 HOH HOH 339 H HOH 340 5 HOH HOH 340 H HOH 341 5 HOH HOH 341 H HOH 342 5 HOH HOH 342 H HOH 343 5 HOH HOH 343 H HOH 344 5 HOH HOH 344 H HOH 346 5 HOH HOH 346 H HOH 347 5 HOH HOH 347 H HOH 298 5 HOH HOH 298 I HOH 299 5 HOH HOH 299 I HOH 301 5 HOH HOH 301 I HOH 303 5 HOH HOH 303 I HOH 304 5 HOH HOH 304 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 3640 -13 13570 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 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 5.66 0.90 118.30 123.96 L L L CB CG OD1 ASP ASP ASP 14 14 14 N L L L 1 -6.68 0.90 118.30 111.62 L L L CB CG OD2 ASP ASP ASP 14 14 14 N 1 -11.18 1.80 110.60 99.42 H H H N CA CB ASP ASP ASP 49 49 49 N 1 -6.69 0.90 118.30 111.61 H H H CB CG OD2 ASP ASP ASP 49 49 49 N E E E 1 5.54 0.90 118.30 123.84 H H H CB CG OD1 ASP ASP ASP 60 60 60 N E E E 1 -7.08 0.90 118.30 111.22 H H H CB CG OD2 ASP ASP ASP 60 60 60 N 1 -3.34 0.50 120.30 116.96 H H H NE CZ NH2 ARG ARG ARG 101 101 101 N 1 -5.74 0.90 118.30 112.56 H H H CB CG OD2 ASP ASP ASP 102 102 102 N 1 -5.68 0.90 118.30 112.62 H H H CB CG OD2 ASP ASP ASP 170 170 170 N 1 5.48 0.90 118.30 123.78 H H H CB CG OD1 ASP ASP ASP 178 178 178 N 1 -6.05 0.90 118.30 112.25 H H H CB CG OD2 ASP ASP ASP 178 178 178 N 1 -6.51 0.90 118.30 111.79 H H H CB CG OD1 ASP ASP ASP 189 189 189 N 1 6.42 0.90 118.30 124.72 H H H CB CG OD2 ASP ASP ASP 189 189 189 N 1 -5.82 0.90 118.30 112.48 H H H CB CG OD1 ASP ASP ASP 194 194 194 N 1 -5.40 0.90 118.30 112.90 H H H CB CG OD2 ASP ASP ASP 243 243 243 N E E 1 L L CD OE1 GLU GLU 14 14 0.071 0.011 1.252 1.323 N 1 H H CD OE2 GLU GLU 18 18 0.073 0.011 1.252 1.325 N 1 H H CD OE2 GLU GLU 39 39 0.070 0.011 1.252 1.322 N 1 H H CD OE2 GLU GLU 86 86 0.069 0.011 1.252 1.321 N A A 1 H H CD OE1 GLU GLU 97 97 0.070 0.011 1.252 1.322 N B B 1 H H CD OE2 GLU GLU 186 186 0.076 0.011 1.252 1.328 N 1 I I CD OE2 GLU GLU 4 4 0.075 0.011 1.252 1.327 N 1 L PHE 7 -126.42 -87.59 1 H SER 48 175.36 166.10 1 H ASP 49 -36.70 -22.82 1 H ARG 50 -146.85 -0.47 1 H HIS 57 -51.74 -5.36 A 1 H TYR 60 -155.91 82.23 C 1 H PRO 60 -35.29 -22.00 G 1 H ASN 60 -154.95 72.57 1 H HIS 71 -123.55 -57.42 B 1 H ASN 149 62.57 -6.77 C 1 H VAL 149 -105.63 71.63 1 H SER 214 -104.45 -73.31 1 H GLN 244 -58.34 6.57 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. 0.151 3.16 25.0 1 0.0 3.16 25.0 50 2417 9 0 2358 0.015 1.93 refinement TNT ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX WITH (DES-AMINO ASP 55) HIRUDIN (RESIDUES 55 - 65) AND BENZAMIDINE 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 2.012 L CYS 1 A SG CYS 9 1_555 H CYS 122 B SG CYS 119 1_555 disulf 2.064 H CYS 42 B SG CYS 28 1_555 H CYS 58 B SG CYS 44 1_555 disulf 2.029 H CYS 168 B SG CYS 173 1_555 H CYS 182 B SG CYS 187 1_555 disulf 2.043 H CYS 191 B SG CYS 201 1_555 H CYS 220 B SG CYS 231 1_555 HYDROLASE/HYDROLASE INHIBITOR SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX H SER 36 B SER 22 A 1 H PRO 37 B PRO 23 0.80 THRB_HUMAN UNP 1 328 P00734 THRB_HUMAN UNP 2 364 P00734 ITHH_HIRME UNP 3 55 P28508 328 363 1DWB 1 14 P00734 H N L 1 1 36 364 622 1DWB 16 247 P00734 H 2 1 259 55 65 1DWB 1 11 P28508 I 3 1 11 7 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel 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 BEN H 1 Software 7 BINDING SITE FOR CHAIN I OF HIRUDIN IIIA Software 18 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 ASP 189 B ASP 199 7 1_555 H ALA 190 B ALA 200 7 1_555 H SER 195 B SER 205 7 1_555 H TRP 215 B TRP 227 7 1_555 H GLY 219 B GLY 230 7 1_555 H GLY 226 B GLY 238 7 1_555 H HOH 325 F HOH 7 1_555 H LYS 36 B LYS 21 18 1_555 H GLN 38 B GLN 24 18 1_555 H ARG 67 B ARG 62 18 1_555 H ARG 73 B ARG 68 18 1_555 H THR 74 B THR 69 18 1_555 H ARG 75 B ARG 70 18 7_555 H ARG 75 B ARG 70 18 1_555 H TYR 76 B TYR 71 18 1_555 H ILE 82 B ILE 78 18 1_555 H MET 84 B MET 80 18 1_555 H LYS 236 B LYS 248 18 3_544 H GLN 239 B GLN 251 18 3_544 H HOH 339 F HOH 18 1_555 I HOH 298 G HOH 18 1_555 I HOH 299 G HOH 18 1_555 I HOH 301 G HOH 18 7_555 I HOH 303 G HOH 18 1_555 I HOH 304 G HOH 18 1_555 96 P 43 21 2