Crystal Structure of Thrombin in complex with compound20a. Determined by X-ray diffraction at 1.79 Å resolution. Released 26 Aug 2020.
Explore 6ZUN in 3D Show helices and sheets RCSB PDB PDBe
6ZUN contains 15 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 |
|---|---|---|---|
| β-strand | 17 | 1 | 1 |
| β-strand | 20-21 | 2 | 2 |
| α-helix | 22-23 | 2 | |
| β-strand | 30-36 | 7 | 3 |
| β-strand | 38-46 | 9 | 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 | 60G-60H | 2 | 4 |
| α-helix | 61-63 | 3 | |
| β-strand | 64-68 | 5 | 3 |
| β-strand | 72 | 1 | 5 |
| β-strand | 81-90 | 10 | 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 | 123-124 | 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 | |
| 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 | 12-15 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14H | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Prothrombin | L | protein | 36 | Homo sapiens | P00734 (AlphaFold model) |
| Prothrombin | H | protein | 259 | Homo sapiens | P00734 (AlphaFold model) |
| Hirudin-2 | I | protein | 11 | Hirudo medicinalis | P28504 (AlphaFold model) |
>6ZUN_1 Prothrombin (chains L) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>6ZUN_2 Prothrombin (chains H) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE
>6ZUN_3 Hirudin-2 (chains I) GDFEEIPEEYL
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| QQ5 | [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-[(3~{R},4~{R})-… | C22 H24 Cl N3 O4 | 1 |
Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics. Hillisch, A., Gericke, K.M., Allerheiligen, S. et al. J Med Chem (2020) 63:12574-12594. DOI 10.1021/acs.jmedchem.0c01035 · 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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