Thrombin Inhibition by Pyridin Derivatives. Determined by X-ray diffraction at 1.35 Å resolution. Released 7 Mar 2012.
Explore 3QX5 in 3D Show helices and sheets RCSB PDB PDBe
3QX5 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 |
|---|---|---|---|
| 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 | 123-124 | 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 | 235-245 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 556-560 | 5 | |
| α-helix | 561-564 | 4 |
| 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 variant-2 | I | protein | 13 | Hirudo medicinalis | P09945 (AlphaFold model) |
>3QX5_1 Thrombin light chain (chains L) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>3QX5_2 Thrombin heavy chain (chains H) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE
>3QX5_3 Hirudin variant-2 (chains I) NGDFEEIPEEYLQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| 02P | D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-2-yl)methyl]-L-prolinamide | C21 H26 Cl N4 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 (GOL, NA) are not listed.
Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin. Biela, A., Khayat, M., Tan, H. et al. J Mol Biol (2012) 418:350-366. DOI 10.1016/j.jmb.2012.01.054 · 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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