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PDBsum entry 5cha

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protein ligands Protein-protein interface(s) links
Hydrolase (serine proteinase) PDB id
5cha
Jmol
Contents
Protein chains
131 a.a. *
97 a.a. *
Ligands
CYS-GLY-VAL-PRO-
ALA-ILE-GLN-PRO-
VAL
×2
Waters ×247
* Residue conservation analysis
PDB id:
5cha
Name: Hydrolase (serine proteinase)
Title: The refinement and the structure of the dimer of alpha- Chymotrypsin at 1.67- Angstroms resolution
Structure: Alpha-chymotrypsin a. Chain: a, e. Alpha-chymotrypsin a. Chain: b, f. Alpha-chymotrypsin a. Chain: c, g. Ec: 3.4.21.1
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organism_taxid: 9913
Biol. unit: Trimer (from PQS)
Resolution:
1.67Å     R-factor:   0.179    
Authors: R.A.Blevins,A.Tulinsky
Key ref: R.A.Blevins and A.Tulinsky (1985). The refinement and the structure of the dimer of alpha-chymotrypsin at 1.67-A resolution. J Biol Chem, 260, 4264-4275. PubMed id: 3980476
Date:
22-Jan-85     Release date:   01-Apr-85    
Supersedes: 3cha
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
Seq:
Struc:
245 a.a.
131 a.a.
Protein chains
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
Seq:
Struc:
245 a.a.
97 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains B, C, F, G: 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!
  Biological process     proteolysis   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
J Biol Chem 260:4264-4275 (1985)
PubMed id: 3980476  
 
 
The refinement and the structure of the dimer of alpha-chymotrypsin at 1.67-A resolution.
R.A.Blevins, A.Tulinsky.
 
  ABSTRACT  
 
The two molecules of the asymmetric unit of the pH 3.5 conformer of alpha-chymotrypsin have been refined at 1.67-A resolution using restrained least squares methods with Hendrickson's program (PROLSQ). The final R factor is 0.179 (including 247 water molecules). The folding of the main chain of the independent molecules is the same within experimental error but the same does not generally apply to the side chain stereochemistry. From this we conclude that the folding of a protein structure is basically independent of most of the detailed stereochemistry of its side chains. The side chains of the interface region between the independent molecules display pronounced asymmetry. This asymmetry suggests that dynamic and asymmetrical structural changes take place at the time of oligomerization leading to more energetically favorable interactions for the dimer. Comparison of the structures of the independent molecules of alpha-chymotrypsin with the structure of monomeric gamma-chymotrypsin revealed that although the folding of the three molecules is essentially the same, numerous and significant differences pervade the side chain stereochemistry attributable to general flexibility. The specificity site of alpha-chymotrypsin is occupied by ordered water molecules in a similar way to gamma-chymotrypsin and other proteins. Some of these water molecules are displaced when substrate binds to the enzyme, while the others appear to help identify and position the aromatic side chain in catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18798568 A.Kernytsky, and B.Rost (2009).
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Variation of atomic charges on proton transfer in strong hydrogen bonds: the case of anionic and neutral imidazole-acetate complexes.
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15778956 D.Segal, and M.Eisenstein (2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
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15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
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15557259 J.Mátrai, G.Verheyden, P.Krüger, and Y.Engelborghs (2004).
Simulation of the activation of alpha-chymotrypsin: analysis of the pathway and role of the propeptide.
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15258613 M.H.Nanao, S.O.Tcherniuk, J.Chroboczek, O.Dideberg, A.Dessen, and M.Y.Balakirev (2004).
Crystal structure of human otubain 2.
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PDB code: 1tff
11847280 A.Heifetz, E.Katchalski-Katzir, and M.Eisenstein (2002).
Electrostatics in protein-protein docking.
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11967357 C.N.Patel, S.M.Noble, G.T.Weatherly, A.Tripathy, D.J.Winzor, and G.J.Pielak (2002).
Effects of molecular crowding by saccharides on alpha-chymotrypsin dimerization.
  Protein Sci, 11, 997.  
10737939 D.W.Ritchie, and G.J.Kemp (2000).
Protein docking using spherical polar Fourier correlations.
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11209755 E.Estébanez-Perpiña, P.Fuentes-Prior, D.Belorgey, M.Braun, R.Kiefersauer, K.Maskos, R.Huber, H.Rubin, and W.Bode (2000).
Crystal structure of the caspase activator human granzyme B, a proteinase highly specific for an Asp-P1 residue.
  Biol Chem, 381, 1203-1214.
PDB code: 1fq3
10500112 C.P.Sommerhoff, W.Bode, P.J.Pereira, M.T.Stubbs, J.Stürzebecher, G.P.Piechottka, G.Matschiner, and A.Bergner (1999).
The structure of the human betaII-tryptase tetramer: fo(u)r better or worse.
  Proc Natl Acad Sci U S A, 96, 10984-10991.  
10328272 G.Moont, H.A.Gabb, and M.J.Sternberg (1999).
Use of pair potentials across protein interfaces in screening predicted docked complexes.
  Proteins, 35, 364-373.  
10328266 S.M.King, and W.C.Johnson (1999).
Assigning secondary structure from protein coordinate data.
  Proteins, 35, 313-320.  
  9568890 A.R.Khan, and M.N.James (1998).
Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes.
  Protein Sci, 7, 815-836.  
9836602 S.R.Presnell, G.S.Patil, C.Mura, K.M.Jude, J.M.Conley, J.A.Bertrand, C.M.Kam, J.C.Powers, and L.D.Williams (1998).
Oxyanion-mediated inhibition of serine proteases.
  Biochemistry, 37, 17068-17081.
PDB codes: 1bju 1bjv
10099253 T.Ke, B.Tidor, and A.M.Klibanov (1998).
Molecular-modeling calculations of enzymatic enantioselectivity taking hydration into account.
  Biotechnol Bioeng, 57, 741-745.  
  9568891 Y.Yan, Y.Li, S.Munshi, V.Sardana, J.L.Cole, M.Sardana, C.Steinkuehler, L.Tomei, R.De Francesco, L.C.Kuo, and Z.Chen (1998).
Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 A resolution structure in a hexagonal crystal form.
  Protein Sci, 7, 837-847.
PDB codes: 1jxp 1ns3
  9300481 A.J.Scheidig, T.R.Hynes, L.A.Pelletier, J.A.Wells, and A.A.Kossiakoff (1997).
Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities.
  Protein Sci, 6, 1806-1824.
PDB codes: 1ca0 1cbw 1taw
  9232643 D.E.Timm (1997).
The crystal structure of the mouse glandular kallikrein-13 (prorenin converting enzyme).
  Protein Sci, 6, 1418-1425.
PDB code: 1ao5
9354616 M.Renatus, M.T.Stubbs, R.Huber, P.Bringmann, P.Donner, W.D.Schleuning, and W.Bode (1997).
Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage.
  Biochemistry, 36, 13483-13493.
PDB code: 1a5i
9188684 P.P.Berna, N.T.Mrabet, J.Van Beeumen, B.Devreese, J.Porath, and M.A.Vijayalakshmi (1997).
Residue accessibility, hydrogen bonding, and molecular recognition: metal-chelate probing of active site histidines in chymotrypsins.
  Biochemistry, 36, 6896-6905.  
  8931142 D.H.Shin, H.K.Song, I.S.Seong, C.S.Lee, C.H.Chung, and S.W.Suh (1996).
Crystal structure analyses of uncomplexed ecotin in two crystal forms: implications for its function and stability.
  Protein Sci, 5, 2236-2247.
PDB codes: 1ecy 1ecz
  8896442 P.Hof, I.Mayr, R.Huber, E.Korzus, J.Potempa, J.Travis, J.C.Powers, and W.Bode (1996).
The 1.8 A crystal structure of human cathepsin G in complex with Suc-Val-Pro-PheP-(OPh)2: a Janus-faced proteinase with two opposite specificities.
  EMBO J, 15, 5481-5491.
PDB code: 1cgh
8808738 R.A.Buono, N.Kucharczyk, M.Neuenschwander, J.Kemmink, L.Y.Hwang, J.L.Fauchère, and C.A.Venanzi (1996).
Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly]
  J Comput Aided Mol Des, 10, 213-232.  
  7535613 B.O.Villoutreix, E.D.Getzoff, and J.H.Griffin (1994).
A structural model for the prostate disease marker, human prostate-specific antigen.
  Protein Sci, 3, 2033-2044.
PDB code: 1pfa
8302861 E.Pizzi, A.Tramontano, L.Tomei, N.La Monica, C.Failla, M.Sardana, T.Wood, and R.De Francesco (1994).
Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition.
  Proc Natl Acad Sci U S A, 91, 888-892.  
  8156987 M.E.McGrath, T.Erpel, C.Bystroff, and R.J.Fletterick (1994).
Macromolecular chelation as an improved mechanism of protease inhibition: structure of the ecotin-trypsin complex.
  EMBO J, 13, 1502-1507.  
7803238 T.Miyata, K.Kuze, T.Matsusue, H.Komooka, K.Kamiya, H.Umeyama, A.Matsui, H.Kato, and A.Yoshioka (1994).
Factor IX Bm Kiryu: a Val-313-to-Asp substitution in the catalytic domain results in loss of function due to a conformational change of the surface loop: evidence obtained by chimaeric modelling.
  Br J Haematol, 88, 156-165.  
7685280 L.C.Petersen, J.J.Birktoft, and H.Flodgaard (1993).
Binding of bovine pancreatic trypsin inhibitor to heparin binding protein/CAP37/azurocidin. Interaction between a Kunitz-type inhibitor and a proteolytically inactive serine proteinase homologue.
  Eur J Biochem, 214, 271-279.  
8451241 N.Vtyurin (1993).
The role of local tight packing of hydrophobic groups in beta-structure.
  Proteins, 15, 62-70.  
8281919 V.Dorovska-Taran, C.Veeger, and A.J.Visser (1993).
Reverse micelles as a water-property-control system to investigate the hydration/activity relationship of alpha-chymotrypsin.
  Eur J Biochem, 218, 1013-1019.  
1557349 J.S.Finer-Moore, A.A.Kossiakoff, J.H.Hurley, T.Earnest, and R.M.Stroud (1992).
Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.
  Proteins, 12, 203-222.
PDB code: 5ptp
  1304905 L.Wesson, and D.Eisenberg (1992).
Atomic solvation parameters applied to molecular dynamics of proteins in solution.
  Protein Sci, 1, 227-235.  
  1321034 N.A.Lokker, M.R.Mark, E.A.Luis, G.L.Bennett, K.A.Robbins, J.B.Baker, and P.J.Godowski (1992).
Structure-function analysis of hepatocyte growth factor: identification of variants that lack mitogenic activity yet retain high affinity receptor binding.
  EMBO J, 11, 2503-2510.  
1729682 S.P.Bajaj, A.K.Sabharwal, J.Gorka, and J.J.Birktoft (1992).
Antibody-probed conformational transitions in the protease domain of human factor IX upon calcium binding and zymogen activation: putative high-affinity Ca(2+)-binding site in the protease domain.
  Proc Natl Acad Sci U S A, 89, 152-156.  
  1304349 W.Bode, D.Turk, and A.Karshikov (1992).
The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.
  Protein Sci, 1, 426-471.
PDB codes: 1ai8 1aix
2017435 A.P.Korn, and R.M.Burnett (1991).
Distribution and complementarity of hydropathy in multisubunit proteins.
  Proteins, 9, 37-55.  
1907667 J.Rose, and F.Eisenmenger (1991).
A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm.
  J Mol Evol, 32, 340-354.  
2381905 J.Greer (1990).
Comparative modeling methods: application to the family of the mammalian serine proteases.
  Proteins, 7, 317-334.  
3228244 L.B.Evnin, and C.S.Craik (1988).
Development of an efficient method for generating and screening active trypsin and trypsin variants.
  Ann N Y Acad Sci, 542, 61-74.  
3237717 M.E.Murphy, J.Moult, R.C.Bleackley, H.Gershenfeld, I.L.Weissman, and M.N.James (1988).
Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes.
  Proteins, 4, 190-204.  
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.