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PDBsum entry 1c1m
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Hydrolase PDB id
1c1m

 

 

 

 

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Contents
Protein chain
240 a.a. *
Ligands
SO4
Metals
_XE
_CA
Waters ×128
* Residue conservation analysis
PDB id:
1c1m
Name: Hydrolase
Title: Porcine elastase under xenon pressure (8 bar)
Structure: Protein (porcine elastase). Chain: a. Ec: 3.4.21.36
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas
Resolution:
2.20Å     R-factor:   0.173     R-free:   0.201
Authors: T.Prange,M.Schiltz,L.Pernot,N.Colloc'H,S.Longhi,W.Bourguet,R.Fourme
Key ref: T.Prangé et al. (1998). Exploring hydrophobic sites in proteins with xenon or krypton. Proteins, 30, 61-73. PubMed id: 9443341
Date:
22-Jul-99     Release date:   28-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00772  (CELA1_PIG) -  Chymotrypsin-like elastase family member 1 from Sus scrofa
Seq:
Struc: 		266 a.a.
240 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.36  - pancreatic elastase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins, including elastin. Preferential cleavage: Ala-|-Xaa.

 

 
Proteins 30:61-73 (1998)
PubMed id: 9443341  
 
 
Exploring hydrophobic sites in proteins with xenon or krypton.
T.Prangé, M.Schiltz, L.Pernot, N.Colloc'h, S.Longhi, W.Bourguet, R.Fourme.
 
  ABSTRACT  
 
X-ray diffraction is used to study the binding of xenon and krypton to a variety of crystallised proteins: porcine pancreatic elastase; subtilisin Carlsberg from Bacillus licheniformis; cutinase from Fusarium solani; collagenase from Hypoderma lineatum; hen egg lysozyme, the lipoamide dehydrogenase domain from the outer membrane protein P64k from Neisseria meningitidis; urate-oxidase from Aspergillus flavus, mosquitocidal delta-endotoxin CytB from Bacillus thuringiensis and the ligand-binding domain of the human nuclear retinoid-X receptor RXR-alpha. Under gas pressures ranging from 8 to 20 bar, xenon is able to bind to discrete sites in hydrophobic cavities, ligand and substrate binding pockets, and into the pore of channel-like structures. These xenon complexes can be used to map hydrophobic sites in proteins, or as heavy-atom derivatives in the isomorphous replacement method of structure determination.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18375516 N.Colloc'h, L.Gabison, G.Monard, M.Altarsha, M.Chiadmi, G.Marassio, J.Sopkova-de Oliveira Santos, M.El Hajji, B.Castro, J.H.Abraini, and T.Prangé (2008).
Oxygen pressurized X-ray crystallography: probing the dioxygen binding site in cofactorless urate oxidase and implications for its catalytic mechanism.
  Biophys J, 95, 2415-2422.
PDB codes: 2zka 2zkb 3cks 3cku
18293927 T.I.Doukov, L.C.Blasiak, J.Seravalli, S.W.Ragsdale, and C.L.Drennan (2008).
Xenon in and at the end of the tunnel of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.
  Biochemistry, 47, 3474-3483.
PDB code: 2z8y
17452791 C.U.Kim, Q.Hao, and S.M.Gruner (2007).
High-pressure cryocooling for capillary sample cryoprotection and diffraction phasing at long wavelengths.
  Acta Crystallogr D Biol Crystallogr, 63, 653-659.
PDB codes: 2oqn 2oqu
17400927 L.Mouawad, C.Tetreau, S.Abdel-Azeim, D.Perahia, and D.Lavalette (2007).
CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations.
  Protein Sci, 16, 781-794.  
17028130 N.Colloc'h, J.Sopkova-de Oliveira Santos, P.Retailleau, D.Vivarès, F.Bonneté, B.Langlois d'Estainto, B.Gallois, A.Brisson, J.J.Risso, M.Lemaire, T.Prangé, and J.H.Abraini (2007).
Protein crystallography under xenon and nitrous oxide pressure: comparison with in vivo pharmacology studies and implications for the mechanism of inhaled anesthetic action.
  Biophys J, 92, 217-224.
PDB codes: 2iba 2ic0 2icq 2ie6 2ie7
16790924 C.U.Kim, Q.Hao, and S.M.Gruner (2006).
Solution of protein crystallographic structures by high-pressure cryocooling and noble-gas phasing.
  Acta Crystallogr D Biol Crystallogr, 62, 687-694.  
16600965 G.E.Gómez, A.Cauerhff, P.O.Craig, F.A.Goldbaum, and J.M.Delfino (2006).
Exploring protein interfaces with a general photochemical reagent.
  Protein Sci, 15, 744-752.  
16131750 J.Ondrácek, M.S.Weiss, J.Brynda, J.Fiala, F.Jursík, P.Rezácová, L.B.Jenner, and J.Sedlácek (2005).
Regular arrangement of periodates bound to lysozyme.
  Acta Crystallogr D Biol Crystallogr, 61, 1181-1189.
PDB code: 1hc0
16214888 S.L.Andrade, A.Dickmanns, R.Ficner, and O.Einsle (2005).
Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus.
  Proc Natl Acad Sci U S A, 102, 14994-14999.
PDB codes: 2b2f 2b2h 2b2i 2b2j
15606769 A.Möglich, B.Koch, W.Gronwald, W.Hengstenberg, E.Brunner, and H.R.Kalbitzer (2004).
Solution structure of the active-centre mutant I14A of the histidine-containing phosphocarrier protein from Staphylococcus carnosus.
  Eur J Biochem, 271, 4815-4824.
PDB code: 1txe
12037300 G.Evans, and G.Bricogne (2002).
Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kalpha X-ray equipment.
  Acta Crystallogr D Biol Crystallogr, 58, 976-991.
PDB codes: 1gw9 1gwa 1gwd 1gwg
11976328 G.H.Addona, S.S.Husain, T.Stehle, and K.W.Miller (2002).
Geometric isomers of a photoactivable general anesthetic delineate a binding site on adenylate kinase.
  J Biol Chem, 277, 25685-25691.  
12198300 M.B.Lascombe, M.Ponchet, P.Venard, M.L.Milat, J.P.Blein, and T.Prangé (2002).
The 1.45 A resolution structure of the cryptogein-cholesterol complex: a close-up view of a sterol carrier protein (SCP) active site.
  Acta Crystallogr D Biol Crystallogr, 58, 1442-1447.
PDB code: 1lri
11173469 A.Cohen, P.Ellis, N.Kresge, and S.M.Soltis (2001).
MAD phasing with krypton.
  Acta Crystallogr D Biol Crystallogr, 57, 233-238.  
11546867 P.Wentworth, L.H.Jones, A.D.Wentworth, X.Zhu, N.A.Larsen, I.A.Wilson, X.Xu, W.A.Goddard, K.D.Janda, A.Eschenmoser, and R.A.Lerner (2001).
Antibody catalysis of the oxidation of water.
  Science, 293, 1806-1811.  
11418770 S.Korolev, I.Dementieva, R.Sanishvili, W.Minor, Z.Otwinowski, and A.Joachimiak (2001).
Using surface-bound rubidium ions for protein phasing.
  Acta Crystallogr D Biol Crystallogr, 57, 1008-1012.  
10828976 U.Langhorst, J.Backmann, R.Loris, and J.Steyaert (2000).
Analysis of a water mediated protein-protein interactions within RNase T1.
  Biochemistry, 39, 6586-6593.  
10666615 Z.Dauter, M.Dauter, and K.R.Rajashankar (2000).
Novel approach to phasing proteins: derivatization by short cryo-soaking with halides.
  Acta Crystallogr D Biol Crystallogr, 56, 232-237.  
16429610 C.R.Bowers, V.Storhaug, C.E.Webster, J.Bharatam, A.Cottone, R.Gianna, K.Betsey, and B.J.Gaffney (1999).
Exploring surfaces and cavities in lipoxygenase and other proteins by hyperpolarized xenon-129 NMR.
  J Am Chem Soc, 121, 9370-9377.  
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 codes are shown on the right.

 

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