Thrombin in complex with (S)-(4-chloro-2-((1-(5-methyl-1H-pyrrole-2-carbonyl)pyrrolidine-2-carboxamido)methyl)phenyl)methanaminium. Determined by X-ray diffraction at 1.5 Å resolution. Released 17 Jun 2015.
Explore 4YES in 3D Show helices and sheets RCSB PDB PDBe
4YES contains 16 α-helices and 24 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 |
|---|---|---|---|
| α-helix | 343-345 | 3 | |
| α-helix | 352-358 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 365 | 1 | 1 |
| β-strand | 368-369 | 2 | 2 |
| α-helix | 370-371 | 2 | |
| β-strand | 378-383 | 6 | 3 |
| β-strand | 388-395 | 8 | 3 |
| β-strand | 400-403 | 4 | 3 |
| α-helix | 405-407 | 3 | |
| β-strand | 409-410 | 2 | 4 |
| α-helix | 411-413 | 3 | |
| β-strand | 415-416 | 2 | 4 |
| α-helix | 419-421 | 3 | |
| β-strand | 422-426 | 5 | 3 |
| β-strand | 430 | 1 | 5 |
| β-strand | 440-449 | 10 | 3 |
| β-strand | 454 | 1 | 6 |
| β-strand | 460 | 1 | 6 |
| β-strand | 464-468 | 5 | 3 |
| α-helix | 471-474 | 4 | |
| β-strand | 475 | 1 | 7 |
| β-strand | 478 | 1 | 7 |
| α-helix | 480-481 | 2 | |
| β-strand | 482 | 1 | 2 |
| α-helix | 486-492 | 7 | |
| β-strand | 498-503 | 6 | 2 |
| β-strand | 522 | 1 | 5 |
| β-strand | 524-530 | 7 | 2 |
| α-helix | 533-538 | 6 | |
| α-helix | 543-545 | 3 | |
| β-strand | 548-551 | 4 | 2 |
| α-helix | 555-557 | 3 | |
| β-strand | 562 | 1 | 1 |
| β-strand | 571-575 | 5 | 2 |
| β-strand | 582-590 | 9 | 2 |
| β-strand | 601-605 | 5 | 2 |
| α-helix | 607-609 | 3 | |
| α-helix | 610-620 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 56-58 | 3 | |
| α-helix | 61-64 | 4 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Thrombin light chain | A | protein | 36 | Homo sapiens | P00734 (AlphaFold model) |
| Thrombin heavy chain | B | protein | 259 | Homo sapiens | P00734 (AlphaFold model) |
| Hirudin | H | protein | 13 | Hirudo medicinalis | P01050 (AlphaFold model) |
>4YES_1 Thrombin light chain (chains A) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>4YES_2 Thrombin heavy chain (chains B) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE
>4YES_3 Hirudin (chains H) XGDFEEIPEEYLQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| MG | Magnesium ion | Mg | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| 45S | N-[2-(aminomethyl)-5-chlorobenzyl]-1-[(5-methyl-1H-pyrrol-2-yl)carbonyl]-L-prol… | C19 H23 Cl N4 O2 | 1 |
Water and common crystallization additives (GOL) are not listed.
Improved Stability of Proline-Derived Direct Thrombin Inhibitors through Hydroxyl to Heterocycle Replacement. Chobanian, H.R., Pio, B., Guo, Y. et al. ACS Med Chem Lett (2015) 6:553-557. DOI 10.1021/acsmedchemlett.5b00047 · 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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