PDBsum entry 1fj3

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Hydrolase PDB id
Protein chain
316 a.a. *
ACN ×2
_CA ×4
Waters ×135
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Thermolysin (50% acetone soaked)
Structure: Thermolysin. Chain: a. Ec:
Source: Bacillus thermoproteolyticus. Organism_taxid: 1427
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.160     R-free:   0.205
Authors: A.C.English,C.R.Groom,R.E.Hubbard
Key ref: A.C.English et al. (2001). Experimental and computational mapping of the binding surface of a crystalline protein. Protein Eng, 14, 47-59. PubMed id: 11287678
07-Aug-00     Release date:   18-Apr-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00800  (THER_BACTH) -  Thermolysin
548 a.a.
316 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Thermolysin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Xaa-|-Leu > Xaa-|-Phe.
      Cofactor: Ca(2+); Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metalloendopeptidase activity     1 term  


Protein Eng 14:47-59 (2001)
PubMed id: 11287678  
Experimental and computational mapping of the binding surface of a crystalline protein.
A.C.English, C.R.Groom, R.E.Hubbard.
Multiple Solvent Crystal Structures (MSCS) is a crystallographic technique to identify energetically favorable positions and orientations of small organic molecules on the surface of proteins. We determined the high-resolution crystal structures of thermolysin (TLN), generated from crystals soaked in 50--70% acetone, 50--80% acetonitrile and 50 mM phenol. The structures of the protein in the aqueous-organic mixtures are essentially the same as the native enzyme and a number of solvent interaction sites were identified. The distribution of probe molecules shows clusters in the main specificity pocket of the active site and a buried subsite. Within the active site, we compared the experimentally determined solvent positions with predictions from two computational functional group mapping techniques, GRID and Multiple Copy Simultaneous Search (MCSS). The experimentally determined small molecule positions are consistent with the structures of known protein--ligand complexes of TLN.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20459833 D.H.Bryant, M.Moll, B.Y.Chen, V.Y.Fofanov, and L.E.Kavraki (2010).
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.
  BMC Bioinformatics, 11, 242.  
19152630 O.A.Adekoya, and I.Sylte (2009).
The thermolysin family (m4) of enzymes: therapeutic and biotechnological potential.
  Chem Biol Drug Des, 73, 7.  
19176554 R.Brenke, D.Kozakov, G.Y.Chuang, D.Beglov, D.Hall, M.R.Landon, C.Mattos, and S.Vajda (2009).
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.
  Bioinformatics, 25, 621-627.  
20333269 R.Powers (2009).
Advances in Nuclear Magnetic Resonance for Drug Discovery.
  Expert Opin Drug Discov, 4, 1077-1098.  
18205727 M.R.Landon, R.E.Amaro, R.Baron, C.H.Ngan, D.Ozonoff, J.A.McCammon, and S.Vajda (2008).
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.
  Chem Biol Drug Des, 71, 106-116.  
18421145 R.E.Hubbard (2008).
Fragment approaches in structure-based drug discovery.
  J Synchrotron Radiat, 15, 227-230.  
17163509 J.Mansfeld, and R.Ulbrich-Hofmann (2007).
The stability of engineered thermostable neutral proteases from Bacillus stearothermophilus in organic solvents and detergents.
  Biotechnol Bioeng, 97, 672-679.  
17139084 W.C.Ho, C.Luo, K.Zhao, X.Chai, M.X.Fitzgerald, and R.Marmorstein (2006).
High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds.
  Acta Crystallogr D Biol Crystallogr, 62, 1484-1493.
PDB codes: 2ioi 2iom 2ioo
15908573 D.Kozakov, K.H.Clodfelter, S.Vajda, and C.J.Camacho (2005).
Optimal clustering for detecting near-native conformations in protein docking.
  Biophys J, 89, 867-875.  
15495260 J.Fernandez-Recio, M.Totrov, C.Skorodumov, and R.Abagyan (2005).
Optimal docking area: a new method for predicting protein-protein interaction sites.
  Proteins, 58, 134-143.  
15608178 S.H.Sheu, D.R.Lancia, K.H.Clodfelter, M.R.Landon, and S.Vajda (2005).
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.
  Nucleic Acids Res, 33, D206-D211.  
14737182 X.I.Ambroggio, D.C.Rees, and R.J.Deshaies (2004).
JAMM: a metalloprotease-like zinc site in the proteasome and signalosome.
  PLoS Biol, 2, E2.
PDB code: 1r5x
15618645 Y.Muta, H.Oneda, and K.Inouye (2004).
Inhibitory effects of alcohols on the activity of human matrix metalloproteinase 7 (matrilysin).
  Biosci Biotechnol Biochem, 68, 2649-2652.  
11904374 S.Dennis, T.Kortvelyesi, and S.Vajda (2002).
Computational mapping identifies the binding sites of organic solvents on proteins.
  Proc Natl Acad Sci U S A, 99, 4290-4295.  
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