Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide. Determined by X-ray diffraction at 1.18 Å resolution. Released 26 Aug 2015.
Explore 5AF9 in 3D Show helices and sheets RCSB PDB PDBe
5AF9 contains 17 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 | 30-35 | 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 | 81-90 | 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 | 123-125 | 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 | 519-523 | 5 | |
| α-helix | 524-526 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 8-10 | 3 | |
| α-helix | 14C-14I | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Thrombin heavy chain | H | protein | 258 | HOMO SAPIENS | P00734 (AlphaFold model) |
| Hirudin variant-2 | I | protein | 12 | HIRUDO MEDICINALIS | P09945 (AlphaFold model) |
| Thrombin light chain | L | protein | 29 | HOMO SAPIENS | P00734 (AlphaFold model) |
>5AF9_1 THROMBIN HEAVY CHAIN (chains H) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFG
>5AF9_2 HIRUDIN VARIANT-2 (chains I) GDFEEIPEEYLQ
>5AF9_3 THROMBIN LIGHT CHAIN (chains L) EADCGLRPLFEKKSLEDKTERELLESYID
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| SJR | 4-methoxy-N-(pyridin-2-yl)benzamide | C13 H12 N2 O2 | 1 |
| PO4 | Phosphate ion | O4 P | 1 |
Water and common crystallization additives (NA, GOL, EDO, DMS) are not listed.
Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why. Ruehmann, E., Betz, M., Heine, A. et al. J Med Chem (2015) 58:6960. DOI 10.1021/ACS.JMEDCHEM.5B00812 · 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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