Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide. Determined by X-ray diffraction at 1.27 Å resolution. Released 7 Jun 2017.
Explore 5JZY in 3D Show helices and sheets RCSB PDB PDBe
5JZY contains 18 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 | 123-125 | 3 | |
| 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 | 557-560 | 4 | |
| α-helix | 561-563 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 1C-1A | 3 | |
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14I | 7 |
| 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 variant-2 | I | protein | 12 | Hirudo medicinalis | P09945 (AlphaFold model) |
>5JZY_1 Prothrombin (chains L) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>5JZY_2 Prothrombin (chains H) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE
>5JZY_3 Hirudin variant-2 (chains I) GDFEEIPEEYLQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| 6OV | 3-cyclohexyl-D-alanyl-N-[(4-carbamimidoylphenyl)methyl]-L-prolinamide | C22 H33 N5 O2 | 1 |
| PO4 | Phosphate ion | O4 P | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Water and common crystallization additives (NA, DMS) are not listed.
Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. Sandner, A., Hufner-Wulsdorf, T., Heine, A. et al. J Med Chem (2019) 62:9753-9771. DOI 10.1021/acs.jmedchem.9b01196 · 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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