PDBsum entry 2gkt

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protein links
Hydrolase inhibitor PDB id
Protein chain
51 a.a. *
Waters ×64
* Residue conservation analysis
PDB id:
Name: Hydrolase inhibitor
Title: Crystal structure of the p14'-ala32 variant of the n- terminally truncated omtky3-del(1-5)
Structure: Ovomucoid. Chain: i. Fragment: turkey ovomucoid third domain del (1-5). Engineered: yes. Mutation: yes
Source: Meleagris gallopavo. Turkey. Organism_taxid: 9103. Expressed in: escherichia coli. Expression_system_taxid: 562
1.23Å     R-factor:   0.132     R-free:   0.151
Authors: T.W.Lee,M.A.Qasim,M.Laskowski Jr.,M.N.G.James
Key ref:
T.W.Lee et al. (2007). Structural insights into the non-additivity effects in the sequence-to-reactivity algorithm for serine peptidases and their inhibitors. J Mol Biol, 367, 527-546. PubMed id: 17266986 DOI: 10.1016/j.jmb.2007.01.008
03-Apr-06     Release date:   13-Feb-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P68390  (IOVO_MELGA) -  Ovomucoid
185 a.a.
51 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     serine-type endopeptidase inhibitor activity     1 term  


DOI no: 10.1016/j.jmb.2007.01.008 J Mol Biol 367:527-546 (2007)
PubMed id: 17266986  
Structural insights into the non-additivity effects in the sequence-to-reactivity algorithm for serine peptidases and their inhibitors.
T.W.Lee, M.A.Qasim, M.Laskowski, M.N.James.
Sequence-to-reactivity algorithms (SRAs) for proteins have the potential of being broadly applied in molecular design. Recently, Laskowski et al. have reported an additivity-based SRA that accurately predicts most of the standard free energy changes of association for variants of turkey ovomucoid third domain (OMTKY3) with six serine peptidases, one of which is streptogrisin B (commonly known as Streptomyces griseus peptidase B, SGPB). Non-additivity effects for residues 18I and 32I, and for residues 20I and 32I of OMTKY3 occurred when the associations with SGPB were predicted using the SRA. To elucidate precisely the mechanics of these non-additivity effects in structural terms, we have determined the crystal structures of the unbound OMTKY3 (with Gly32I as in the wild-type amino acid sequence) at a resolution of 1.16 A, the unbound Ala32I variant of OMTKY3 at a resolution of 1.23 A, and the SGPB:OMTKY3-Ala32I complex (equilibrium association constant K(a)=7.1x10(9) M(-1) at 21(+/-2) C degrees, pH 8.3) at a resolution of 1.70 A. Extensive comparisons with the crystal structure of the unbound OMTKY3 confirm our understanding of some previously addressed non-additivity effects. Unexpectedly, SGPB and OMTKY3-Ala32I form a 1:2 complex in the crystal. Comparison with the SGPB:OMTKY3 complex shows a conformational change in the SGPB:OMTKY3-Ala32I complex, resulting from a hinged rigid-body rotation of the inhibitor caused by the steric hindrance between the methyl group of Ala32IA of the inhibitor and Pro192BE of the peptidase. This perturbs the interactions among residues 18I, 20I, 32I and 36I of the inhibitor, probably resulting in the above non-additivity effects. This conformational change also introduces residue 10I as an additional hyper-variable contact residue to the SRA.
  Selected figure(s)  
Figure 3.
Figure 3. Electron density map of the unbound OMTKY3-Ala32I. (a) 2|F[o]|−|F[c]|,α[c] map of Tyr31I and Ala32I contoured at 3.0σ. (b) 2|F[o]|−|F[c]|,α[c] map of Leu18I and Glu19I contoured at 1.0σ.
Figure 5.
Figure 5. Interactions among Thr17I, Glu19I and Arg21I of ovomucoid third domains under different conditions. (a) Unbound wtOMSVP3.^12 (b) Unbound OMTKY3. (c) SGPB-bound OMTKY3.^22 (d) Unbound OMTKY3-Ala32I. (e) Molecule A of OMTKY3-Ala32I in the SGPB:OMTKY3-Ala32I complex. Hydrogen bonds and ionic interactions are indicated by dotted lines. Water molecules are indicated by w.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 527-546) copyright 2007.  
  Figures were selected by an automated process.