Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK. Determined by X-ray diffraction at 2.34 Å resolution. Released 29 Mar 2017.
Explore 5TO3 in 3D Show helices and sheets RCSB PDB PDBe
5TO3 contains 19 α-helices and 35 β-strands across 2 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 |
|---|---|---|---|
| α-helix | 10-13 | 4 | |
| α-helix | 17-19 | 3 | |
| α-helix | 27-29 | 3 | |
| α-helix | 36-43 | 8 |
| 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 | 40-47 | 8 | 3 |
| β-strand | 52-55 | 4 | 3 |
| α-helix | 57-60 | 4 | |
| β-strand | 61-62 | 2 | 4 |
| α-helix | 63-65 | 3 | |
| β-strand | 67-68 | 2 | 4 |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 3 |
| β-strand | 82 | 1 | 5 |
| β-strand | 92-94 | 3 | 3 |
| β-strand | 96-101 | 6 | 3 |
| β-strand | 106 | 1 | 6 |
| β-strand | 112 | 1 | 6 |
| β-strand | 116-120 | 5 | 3 |
| α-helix | 123-126 | 4 | |
| α-helix | 132-133 | 2 | |
| β-strand | 134 | 1 | 2 |
| α-helix | 135-136 | 2 | |
| α-helix | 138-144 | 7 | |
| β-strand | 150-155 | 6 | 2 |
| β-strand | 174 | 1 | 5 |
| β-strand | 176-183 | 8 | 2 |
| α-helix | 185-190 | 6 | |
| β-strand | 200-203 | 4 | 2 |
| α-helix | 207-209 | 3 | |
| β-strand | 214 | 1 | 1 |
| β-strand | 223-227 | 5 | 2 |
| β-strand | 234-242 | 9 | 2 |
| β-strand | 253-257 | 5 | 2 |
| α-helix | 259-261 | 3 | |
| α-helix | 262-272 | 11 | |
| α-helix | 350-352 | 3 | |
| β-strand | 359-362 | 4 | 7 |
| β-strand | 368-371 | 4 | 7 |
| β-strand | 376-379 | 4 | 8 |
| β-strand | 382-388 | 7 | 8 |
| β-strand | 394-396 | 3 | 9 |
| β-strand | 398-400 | 3 | 10 |
| α-helix | 401-403 | 3 | |
| β-strand | 405-408 | 4 | 10 |
| β-strand | 413-416 | 4 | 9 |
| β-strand | 420-423 | 4 | 9 |
| α-helix | 426-429 | 4 | |
| β-strand | 436-440 | 5 | 11 |
| β-strand | 443-447 | 5 | 11 |
| β-strand | 456-458 | 3 | 11 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Prothrombin | A | protein | 46 | Homo sapiens | P00734 (AlphaFold model) |
| Prothrombin,Thrombomodulin | B | protein | 409 | Homo sapiens | P00734 (AlphaFold model), P07204 (AlphaFold model) |
>5TO3_1 Prothrombin (chains A) SEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
>5TO3_2 Prothrombin,Thrombomodulin (chains B) IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSAGAGCDRDGKYGFY THVFRLKKWIQKVIDQFGGGSSSAGGGSSSGGGGSSSAGGGSSSGGGGVEPVDPCFRANC EYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQMFCNQTACPADCDPNTQASCECPEGYILD DGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALARHIGTDCDSG
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
| 0G6 | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexa… | C21 H34 Cl N6 O3 | 1 |
Water and common crystallization additives (NA, K) are not listed.
Rational Design of Protein C Activators. Barranco-Medina, S., Murphy, M., Pelc, L. et al. Sci Rep (2017) 7:44596-44596. DOI 10.1038/srep44596 · PubMed
Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 5TO3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.