5TO3
Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Prothrombin | polymer | 46 | 5367.9 | 1 | UniProt (P00734) Pfam (PF09396) | Homo sapiens (Human) | Coagulation factor II |
| 2 | B (B) | Prothrombin,Thrombomodulin | polymer | 409 | 44619.2 | 1 | UniProt (P00734) UniProt (P07204) Pfam (PF00089) Pfam (PF12662) | Homo sapiens (Human) | Coagulation factor II,TM,Fetomodulin |
| 3 | C (C) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1235.1 | 1 | In PDB GlyTouCan (G20640NX) | |||
| 4 | D (B) | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide | non-polymer | 454.0 | 1 | BIRD (PRD_000020) Chemie (0G6) | |||
| 5 | E (B) | POTASSIUM ION | non-polymer | 39.1 | 1 | Chemie (K) | |||
| 6 | F (B) | SODIUM ION | non-polymer | 23.0 | 1 | Chemie (NA) | |||
| 7 | G, H (B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 2 | Chemie (NAG) | |||
| 8 | I, J (A, B) | water | water | 18.0 | 93 | Chemie (HOH) |
Sequence modifications
B: 16 - 273 (UniProt: P00734)
B: 345 - 465 (UniProt: P07204)
| PDB | External Database | Details |
|---|---|---|
| Ala 242 | Trp 590 | engineered mutation |
| Ala 244 | Glu 592 | engineered mutation |
| Gly 274 | - | linker |
| Gly 275 | - | linker |
| Ser 276 | - | linker |
| Ser 318 | - | linker |
| Ser 319 | - | linker |
| Ala 320 | - | linker |
| Gly 321 | - | linker |
| Gly 322 | - | linker |
| Gly 323 | - | linker |
| Ser 324 | - | linker |
| Ser 325 | - | linker |
| Ser 326 | - | linker |
| Gly 327 | - | linker |
| Gly 328 | - | linker |
| Gly 329 | - | linker |
| Gly 330 | - | linker |
| Ser 331 | - | linker |
| Ser 332 | - | linker |
| Ser 333 | - | linker |
| Ala 334 | - | linker |
| Gly 335 | - | linker |
| Gly 336 | - | linker |
| Gly 337 | - | linker |
| Ser 338 | - | linker |
| Ser 339 | - | linker |
| Ser 340 | - | linker |
| Gly 341 | - | linker |
| Gly 342 | - | linker |
| Gly 343 | - | linker |
| Gly 344 | - | linker |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total formula weight | 49987.1 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 1235.1 | |
| Non-Polymers* | Number of molecules | 5 |
| Total formula weight | 958.5 | |
| All* | Total formula weight | 52180.7 |
