2zgx Summary

pdbe.org/2zgx
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Thrombin Inhibition

The structure was published by Baum, B., Muley, L., Heine, A., Smolinski, M., Hangauer, D., and Klebe, G., in 2009 in a paper entitled "Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.8 Å and deposited in 2008.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely Thrombin Light Chain, Thrombin heavy chain, and Hirudin variant-1.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotrimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
L Thrombin Light Chain P00734 (328-363) (THRB_HUMAN)search Homo sapienssearch 93% 36 75%
H Thrombin heavy chain P00734 (364-622) (THRB_HUMAN)search Homo sapienssearch 93% 259 96%
I Hirudin variant-1 P01050 (54-64) (HIRV1_HIRME)search Hirudo medicinalissearch 97% 11 90%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P00734 (328 - 363) Thrombin Light Chain Homo sapiens
P01050 (54 - 64) Hirudin variant-1 Hirudo medicinalis,

Chain Structural classification (CATH) Sequence family (Pfam)
L (P00734) PF09396: Thrombin light chainsearch
H (P00734) Trypsin-like serine proteasessearch PF00089: Trypsinsearch
I (P01050) PF00713: Hirudinsearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
L (P00734) proteolysissearch blood coagulationsearch serine-type endopeptidase activitysearch extracellular regionsearch
H (P00734) proteolysissearch blood coagulationsearch calcium ion bindingsearch serine-type endopeptidase activitysearch catalytic activitysearch

Chain InterPro annotation
L Thrombin light chainsearch
H Peptidase S1search Peptidase S1A, chymotrypsin-typesearch Prothrombin/thrombinsearch Trypsin-like cysteine/serine peptidase domainsearch Peptidase S1, trypsin family, active sitesearch
I