Human Thrombin in complex with MI003. Determined by X-ray diffraction at 1.23 Å resolution. Released 25 Apr 2012.
Explore 3RM2 in 3D Show helices and sheets RCSB PDB PDBe
3RM2 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 | 30-36 | 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 | 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 | |
| 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 | 56-60 | 5 | |
| α-helix | 61-63 | 3 |
| 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) |
>3RM2_1 Thrombin Light Chain (chains L) TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>3RM2_2 Thrombin Heavy Chain (chains H) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE
>3RM2_3 Hirudin variant-2 (chains I) NGDFEEIPEEYLQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| PO4 | Phosphate ion | O4 P | 1 |
| S00 | N-(benzylsulfonyl)-3-cyclohexyl-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide | C29 H39 N5 O4 S | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Water and common crystallization additives (GOL, NA) are not listed.
Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect. Biela, A., Sielaff, F., Terwesten, F. et al. J Med Chem (2012) 55:6094-6110. DOI 10.1021/jm300337q · 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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