Complex of recombinant human thrombin with a designed fluorinated inhibitor. Determined by X-ray diffraction at 1.67 Å resolution. Released 24 Jun 2003.
Explore 1OYT in 3D Show helices and sheets RCSB PDB PDBe
1OYT contains 15 α-helices and 25 β-strands across 3 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 |
|---|---|---|---|
| β-strand | 17 | 1 | 1 |
| β-strand | 20-21 | 2 | 2 |
| α-helix | 22-23 | 2 | |
| β-strand | 30-35 | 6 | 3 |
| β-strand | 39-46 | 8 | 3 |
| β-strand | 51-54 | 4 | 3 |
| α-helix | 56-58 | 3 | |
| β-strand | 60-60A | 2 | 4 |
| α-helix | 60B-60D | 3 | |
| β-strand | 60F-60G | 2 | 4 |
| α-helix | 61-63 | 3 | |
| β-strand | 64-68 | 5 | 3 |
| β-strand | 72 | 1 | 5 |
| β-strand | 81-83 | 3 | 3 |
| β-strand | 85-90 | 6 | 3 |
| β-strand | 95 | 1 | 6 |
| β-strand | 100 | 1 | 6 |
| β-strand | 104-108 | 5 | 3 |
| α-helix | 111-114 | 4 | |
| β-strand | 115 | 1 | 7 |
| β-strand | 118 | 1 | 7 |
| α-helix | 120-121 | 2 | |
| β-strand | 122 | 1 | 2 |
| α-helix | 126-129C | 7 | |
| β-strand | 135-140 | 6 | 2 |
| β-strand | 154 | 1 | 5 |
| β-strand | 156-162 | 7 | 2 |
| α-helix | 165-170 | 6 | |
| α-helix | 175-176 | 2 | |
| β-strand | 180-183 | 4 | 2 |
| α-helix | 186-186B | 3 | |
| β-strand | 189 | 1 | 1 |
| β-strand | 198-202 | 5 | 2 |
| β-strand | 207-215 | 9 | 2 |
| β-strand | 226-230 | 5 | 2 |
| α-helix | 232-234 | 3 | |
| α-helix | 235-244 | 10 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 3-5 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14I | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| thrombin light chain | L | protein | 36 | Homo sapiens | P00734 (AlphaFold model) |
| thrombin heavy chain | H | protein | 259 | Homo sapiens | P00734 (AlphaFold model) |
| Hirudin IIB | I | protein | 11 | Hirudo medicinalis | P28506 (AlphaFold model) |
>1OYT_1 thrombin light chain (chains L) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>1OYT_2 thrombin heavy chain (chains H) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE
>1OYT_3 Hirudin IIB (chains I) XFEEIPEEYLQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| FSN | (3ASR,4RS,8ASR,8BRS)-4-(2-(4-fluorobenzyl)-1,3-DIOXODEACAHYDROPYRROLO[3,4-a]… | C23 H24 F N4 O2 | 1 |
| CA | Calcium ion | Ca | 1 |
Water and common crystallization additives (NA) are not listed.
A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of an Enzyme Active Site: Evidence for CF...C=O Interactions. Olsen, J.A., Banner, D.W., Seiler, P. et al. Angew Chem Int Ed Engl (2003) 42:2507-2511. DOI 10.1002/anie.200351268 · 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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