Thrombin in complex with natural product inhibitor Oscillarin. Determined by X-ray diffraction at 2.04 Å resolution. Released 9 Nov 2004.
Explore 1RIW in 3D Show helices and sheets RCSB PDB PDBe
1RIW contains 17 α-helices and 22 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 16-18 | 3 | |
| α-helix | 25-31 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 38 | 1 | 1 |
| β-strand | 41-42 | 2 | 2 |
| α-helix | 43-44 | 2 | |
| β-strand | 51-56 | 6 | 3 |
| β-strand | 61-68 | 8 | 3 |
| β-strand | 73-76 | 4 | 3 |
| α-helix | 78-80 | 3 | |
| β-strand | 82-83 | 2 | 4 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 92-94 | 3 | |
| β-strand | 95-99 | 5 | 3 |
| β-strand | 103 | 1 | 5 |
| β-strand | 113-122 | 10 | 3 |
| β-strand | 127 | 1 | 6 |
| β-strand | 133 | 1 | 6 |
| β-strand | 137-141 | 5 | 3 |
| α-helix | 144-147 | 4 | |
| α-helix | 153-154 | 2 | |
| β-strand | 155 | 1 | 2 |
| α-helix | 159-165 | 7 | |
| β-strand | 171-176 | 6 | 2 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 189 | 1 | 5 |
| β-strand | 191-197 | 7 | 2 |
| α-helix | 198-199 | 2 | |
| α-helix | 200-205 | 6 | |
| α-helix | 210-211 | 2 | |
| β-strand | 215-218 | 4 | 2 |
| α-helix | 222-224 | 3 | |
| β-strand | 229 | 1 | 1 |
| β-strand | 238-242 | 5 | 2 |
| β-strand | 249-257 | 9 | 2 |
| β-strand | 268-272 | 5 | 2 |
| α-helix | 274-276 | 3 | |
| α-helix | 277-285 | 9 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 356-359 | 4 | |
| α-helix | 361-363 | 3 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| thrombin light chain | A | protein | 36 | Homo sapiens | P00734 (AlphaFold model) |
| thrombin heavy chain, B | B | protein | 147 | Homo sapiens | P00734 (AlphaFold model) |
| thrombin heavy chain, C | C | protein | 105 | Homo sapiens | P00734 (AlphaFold model) |
| Hirudin IIB | D | protein | 11 | Hirudo medicinalis | P28504 (AlphaFold model) |
>1RIW_1 thrombin light chain (chains A) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>1RIW_2 thrombin heavy chain, B (chains B) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKET
>1RIW_3 thrombin heavy chain, C (chains C) GQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSP FNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
>1RIW_4 Hirudin IIB (chains D) DFEEIPEEYLQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| OSC | (2R,3AS,6R,7AS)-N-(2-{1-[amino(imino)methyl]-2,5-dihydro-1H-pyrrol-3-yl}ethyl)-… | C34 H44 N6 O5 | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Water and common crystallization additives (NA) are not listed.
The N-acyloxyiminium ion aza-Prins route to octahydroindoles: total synthesis and structural confirmation of the antithrombotic marine natural product oscillarin. Hanessian, S., Tremblay, M., Petersen, J.F.W. J Am Chem Soc (2004) 126:6064-6071. DOI 10.1021/ja030669g · PubMed
Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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