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PDBsum entry 1acb

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protein Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
1acb
Jmol
Contents
Protein chains
241 a.a. *
63 a.a. *
Waters ×142
* Residue conservation analysis
PDB id:
1acb
Name: Hydrolase/hydrolase inhibitor
Title: Crystal and molecular structure of the bovine alpha-chymotry c complex at 2.0 angstroms resolution
Structure: Alpha-chymotrypsin. Chain: e. Engineered: yes. Eglin c. Chain: i. Engineered: yes
Source: Bos taurus. Bovine. Organism_taxid: 9913. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.167    
Authors: M.Bolognesi,F.Frigerio,A.Coda,L.Pugliese,C.Lionetti,E.Menega G.Amiconi,H.P.Schnebli,P.Ascenzi
Key ref: F.Frigerio et al. (1992). Crystal and molecular structure of the bovine alpha-chymotrypsin-eglin c complex at 2.0 A resolution. J Mol Biol, 225, 107-123. PubMed id: 1583684
Date:
08-Nov-91     Release date:   31-Oct-93    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
Seq:
Struc:
245 a.a.
241 a.a.
Protein chain
Pfam   ArchSchema ?
P01051  (ICIC_HIRME) -  Eglin C
Seq:
Struc:
70 a.a.
63 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain E: E.C.3.4.21.1  - Chymotrypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Tyr-|-Xaa, Trp-|-Xaa, Phe-|-Xaa, Leu-|-Xaa.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     digestion   5 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
J Mol Biol 225:107-123 (1992)
PubMed id: 1583684  
 
 
Crystal and molecular structure of the bovine alpha-chymotrypsin-eglin c complex at 2.0 A resolution.
F.Frigerio, A.Coda, L.Pugliese, C.Lionetti, E.Menegatti, G.Amiconi, H.P.Schnebli, P.Ascenzi, M.Bolognesi.
 
  ABSTRACT  
 
The crystal structure of the complex between bovine alpha-chymotrypsin and the leech (Hirudo medicinalis) protein proteinase inhibitor eglin c has been refined at 2.0 A resolution to a crystallographic R-factor of 0.167. The structure of the complex includes 2290 protein and 143 solvent atoms. Eglin c is bound to the cognate enzyme through interactions involving 11 residues of the inhibitor (sites P5-P4' in the reactive site loop, P10' and P23') and 17 residues from chymotrypsin. Binding of eglin c to the enzyme causes a contained hinge-bending movement around residues P4 and P4' of the inhibitor. The tertiary structure of chymotrypsin is little affected, with the exception of the 10-13 region, where an ordered structure for the polypeptide chain is observed. The overall binding mode is consistent with those found in other serine proteinase-protein-inhibitor complexes, including those from different inhibition families. Contained, but significant differences are observed in the establishment of intramolecular hydrogen bonds and polar interactions stabilizing the structure of the intact inhibitor, if the structure of eglin c in its complex with chymotrypsin is compared with that of other eglin c-serine proteinase complexes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287622 M.J.Whitley, and A.L.Lee (2011).
Exploring the role of structure and dynamics in the function of chymotrypsin inhibitor 2.
  Proteins, 79, 916-924.  
17729269 A.May, and M.Zacharias (2008).
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.
  Proteins, 70, 794-809.  
18658209 N.Rezaei-Ghaleh, M.Amininasab, and M.Nemat-Gorgani (2008).
Conformational changes of alpha-chymotrypsin in a fibrillation-promoting condition: a molecular dynamics study.
  Biophys J, 95, 4139-4147.  
17691895 B.Y.Chen, V.Y.Fofanov, D.H.Bryant, B.D.Dodson, D.M.Kristensen, A.M.Lisewski, M.Kimmel, O.Lichtarge, and L.E.Kavraki (2007).
The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.
  J Comput Biol, 14, 791-816.  
17094110 C.Oliva, A.Rodríguez, M.González, and W.Yang (2007).
A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate.
  Proteins, 66, 444-455.  
17362087 M.R.Yun, N.Mousseau, and P.Derreumaux (2007).
Sampling small-scale and large-scale conformational changes in proteins and molecular complexes.
  J Chem Phys, 126, 105101.  
16342264 J.S.Fetrow, S.T.Knutson, and M.H.Edgell (2006).
Mutations in alpha-helical solvent-exposed sites of eglin c have long-range effects: evidence from molecular dynamics simulations.
  Proteins, 63, 356-372.  
15923225 M.V.Petoukhov, and D.I.Svergun (2005).
Global rigid body modeling of macromolecular complexes against small-angle scattering data.
  Biophys J, 89, 1237-1250.  
15654893 N.Singh, T.Jabeen, S.Sharma, I.Roy, M.N.Gupta, S.Bilgrami, R.K.Somvanshi, S.Dey, M.Perbandt, C.Betzel, A.Srinivasan, and T.P.Singh (2005).
Detection of native peptides as potent inhibitors of enzymes. Crystal structure of the complex formed between treated bovine alpha-chymotrypsin and an autocatalytically produced fragment, IIe-Val-Asn-Gly-Glu-Glu-Ala-Val-Pro-Gly-Ser-Trp-Pro-Trp, at 2.2 angstroms resolution.
  FEBS J, 272, 562-572.
PDB code: 1oxg
16038610 T.S.Zamolodchikova, E.V.Smirnova, A.N.Andrianov, I.V.Kashparov, O.D.Kotsareva, E.A.Sokolova, K.B.Ignatov, and A.D.Pemberton (2005).
Cloning and molecular modeling of duodenase with respect to evolution of substrate specificity within mammalian serine proteases that have lost a conserved active-site disulfide bond.
  Biochemistry (Mosc), 70, 672-684.  
  20526429 C.Yan, V.Honavar, and D.Dobbs (2004).
Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach.
  Neural Comput Appl, 13, 123-129.  
14665623 I.Botos, E.E.Melnikov, S.Cherry, J.E.Tropea, A.G.Khalatova, F.Rasulova, Z.Dauter, M.R.Maurizi, T.V.Rotanova, A.Wlodawer, and A.Gustchina (2004).
The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site.
  J Biol Chem, 279, 8140-8148.
PDB codes: 1rr9 1rre
15606919 T.Z.Sen, A.Kloczkowski, R.L.Jernigan, C.Yan, V.Honavar, K.M.Ho, C.Z.Wang, Y.Ihm, H.Cao, X.Gu, and D.Dobbs (2004).
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.
  BMC Bioinformatics, 5, 205.  
10736156 W.Y.Lu, M.A.Starovasnik, J.J.Dwyer, A.A.Kossiakoff, S.B.Kent, and W.Lu (2000).
Deciphering the role of the electrostatic interactions involving Gly70 in eglin C by total chemical protein synthesis.
  Biochemistry, 39, 3575-3584.  
10328267 J.K.Dattagupta, A.Podder, C.Chakrabarti, U.Sen, D.Mukhopadhyay, S.K.Dutta, and M.Singh (1999).
Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site.
  Proteins, 35, 321-331.
PDB code: 2wbc
10223294 K.E.Knobe, A.Berntsdotter, L.Shen, J.Morser, B.Dahlbäck, and B.O.Villoutreix (1999).
Probing the activation of protein C by the thrombin-thrombomodulin complex using structural analysis, site-directed mutagenesis, and computer modeling.
  Proteins, 35, 218-234.  
10353824 M.A.Qasim, S.M.Lu, J.Ding, K.S.Bateman, M.N.James, S.Anderson, J.Song, J.L.Markley, P.J.Ganz, C.W.Saunders, and M.Laskowski (1999).
Thermodynamic criterion for the conformation of P1 residues of substrates and of inhibitors in complexes with serine proteinases.
  Biochemistry, 38, 7142-7150.  
10381402 W.Lu, M.Randal, A.Kossiakoff, and S.B.Kent (1999).
Probing intermolecular backbone H-bonding in serine proteinase-protein inhibitor complexes.
  Chem Biol, 6, 419-427.  
9521649 C.M.Lukacs, H.Rubin, and D.W.Christianson (1998).
Engineering an anion-binding cavity in antichymotrypsin modulates the "spring-loaded" serpin-protease interaction.
  Biochemistry, 37, 3297-3304.
PDB codes: 1as4 3caa 4caa
9708981 F.Martin, N.Dimasi, C.Volpari, C.Perrera, S.Di Marco, M.Brunetti, C.Steinkühler, R.De Francesco, and M.Sollazzo (1998).
Design of selective eglin inhibitors of HCV NS3 proteinase.
  Biochemistry, 37, 11459-11468.  
9675278 J.Polanowska, I.Krokoszynska, H.Czapinska, W.Watorek, M.Dadlez, and J.Otlewski (1998).
Specificity of human cathepsin G.
  Biochim Biophys Acta, 1386, 189-198.  
9179777 C.Capasso, M.Rizzi, E.Menegatti, P.Ascenzi, and M.Bolognesi (1997).
Crystal structure of the bovine alpha-chymotrypsin:Kunitz inhibitor complex. An example of multiple protein:protein recognition sites.
  J Mol Recognit, 10, 26-35.
PDB code: 1mtn
9048543 M.A.Qasim, P.J.Ganz, C.W.Saunders, K.S.Bateman, M.N.James, and M.Laskowski (1997).
Interscaffolding additivity. Association of P1 variants of eglin c and of turkey ovomucoid third domain with serine proteinases.
  Biochemistry, 36, 1598-1607.  
8679538 B.F.Le Bonniec, T.Myles, T.Johnson, C.G.Knight, C.Tapparelli, and S.R.Stone (1996).
Characterization of the P2' and P3' specificities of thrombin using fluorescence-quenched substrates and mapping of the subsites by mutagenesis.
  Biochemistry, 35, 7114-7122.  
  8732755 B.O.Villoutreix, H.Lilja, K.Pettersson, T.Lövgren, and O.Teleman (1996).
Structural investigation of the alpha-1-antichymotrypsin: prostate-specific antigen complex by comparative model building.
  Protein Sci, 5, 836-851.  
8718849 E.S.Stavridi, K.O'Malley, C.M.Lukacs, W.T.Moore, J.D.Lambris, D.W.Christianson, H.Rubin, and B.S.Cooperman (1996).
Structural change in alpha-chymotrypsin induced by complexation with alpha 1-antichymotrypsin as seen by enhanced sensitivity to proteolysis.
  Biochemistry, 35, 10608-10615.  
7716167 J.Janin (1995).
Elusive affinities.
  Proteins, 21, 30-39.  
8569452 P.Ascenzi, G.Amiconi, W.Bode, M.Bolognesi, M.Coletta, and E.Menegatti (1995).
Proteinase inhibitors from the European medicinal leech Hirudo medicinalis: structural, functional and biomedical aspects.
  Mol Aspects Med, 16, 215-313.  
7807552 L.L.Beuning, T.W.Spriggs, and J.T.Christeller (1994).
Evolution of the proteinase inhibitor I family and apparent lack of hypervariability in the proteinase contact loop.
  J Mol Evol, 39, 644-654.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.