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PDBsum entry 1d7j

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1d7j
Jmol
Contents
Protein chains
107 a.a. *
Ligands
NH4 ×2
SO4 ×2
BUQ ×2
Waters ×129
* Residue conservation analysis
PDB id:
1d7j
Name: Isomerase
Title: Fkbp complexed with 4-hydroxy-2-butanone
Structure: Protein (fk506-binding protein). Chain: a, b. Synonym: fkbp-12. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.85Å     R-factor:   0.191     R-free:   0.254
Authors: P.Burkhard,P.Taylor,M.D.Walkinshaw
Key ref:
P.Burkhard et al. (2000). X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies. J Mol Biol, 295, 953-962. PubMed id: 10656803 DOI: 10.1006/jmbi.1999.3411
Date:
18-Oct-99     Release date:   21-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P62942  (FKB1A_HUMAN) -  Peptidyl-prolyl cis-trans isomerase FKBP1A
Seq:
Struc:
108 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.2.1.8  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   7 terms 
  Biological process     chaperone-mediated protein folding   26 terms 
  Biochemical function     ion channel binding     14 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1999.3411 J Mol Biol 295:953-962 (2000)
PubMed id: 10656803  
 
 
X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies.
P.Burkhard, P.Taylor, M.D.Walkinshaw.
 
  ABSTRACT  
 
A new crystal form of native FK506 binding protein (FKBP) has been obtained which has proved useful in ligand binding studies. Three different small molecule ligand complexes and the native enzyme have been determined at higher resolution than 2.0 A. Dissociation constants of the related small molecule ligands vary from 20 mM for dimethylsulphoxide to 200 microM for tetrahydrothiophene 1-oxide. Comparison of the four available crystal structures shows that the protein structures are identical to within experimental error, but there are differences in the water structure in the active site. Analysis of the calculated buried surface areas of these related ligands provides an estimated van der Waals contribution to the binding energy of -0.5 kJ/A(2) for non-polar interactions between ligand and protein.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. View along the 2-fold axis. One potein molecule is shown in white with its symmetry-related molecule in yellow. On top, His87 forms a hydrogen bond accross the 2-fold axis to the very same histidine of the symmetry-related molecule. The ammonium ion (middle) and the sulphate ion (bottom) are involved in a hydrogen bonding network between the two symmetry-related molecules.
Figure 3.
Figure 3. Superposition of the structures of the native enzyme (cyan) and the FKBP-FK506 complex (yellow). (a) Global view; (b) close-up view. The interatomic distances of the native enzyme are displayed in orange. Distances in the FK506 complex are in light blue. The active site cleft accommodates the structure of the inhibitor FK506 and is wider but shorter in the FK506 complex compared to the native enzyme.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 295, 953-962) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20623657 C.Shyu, and F.M.Ytreberg (2011).
Accurate estimation of solvation free energy using polynomial fitting techniques.
  J Comput Chem, 32, 134-141.  
19405629 F.M.Ytreberg (2009).
Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations.
  J Chem Phys, 130, 164906.  
18704951 S.Szep, S.Park, E.T.Boder, G.D.Van Duyne, and J.G.Saven (2009).
Structural coupling between FKBP12 and buried water.
  Proteins, 74, 603-611.
PDB codes: 2ppn 2ppo 2ppp
17541991 C.H.Röhrig, C.Loch, J.Y.Guan, G.Siegal, and M.Overhand (2007).
Fragment-Based Synthesis and SAR of Modified FKBP Ligands: Influence of Different Linking on Binding Affinity.
  ChemMedChem, 2, 1054-1070.  
16284269 M.S.Lee, and M.A.Olson (2006).
Calculation of absolute protein-ligand binding affinity using path and endpoint approaches.
  Biophys J, 90, 864-877.  
15937899 S.Park, and J.G.Saven (2005).
Statistical and molecular dynamics studies of buried waters in globular proteins.
  Proteins, 60, 450-463.  
14993672 G.Kontopidis, P.Taylor, and M.D.Walkinshaw (2004).
Enzymatic and structural characterization of non-peptide ligand-cyclophilin complexes.
  Acta Crystallogr D Biol Crystallogr, 60, 479-485.
PDB codes: 1w8l 1w8m 1w8v
14695250 J.M.Swanson, R.H.Henchman, and J.A.McCammon (2004).
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy.
  Biophys J, 86, 67-74.  
12579579 J.H.Lin, A.L.Perryman, J.R.Schames, and J.A.McCammon (2003).
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
  Biopolymers, 68, 47-62.  
12737821 N.R.Zaccai, K.Maenaka, T.Maenaka, P.R.Crocker, R.Brossmer, S.Kelm, and E.Y.Jones (2003).
Structure-guided design of sialic acid-based Siglec inhibitors and crystallographic analysis in complex with sialoadhesin.
  Structure, 11, 557-567.
PDB codes: 1od7 1od9 1oda
11751578 P.J.Pereira, M.C.Vega, E.González-Rey, R.Fernández-Carazo, S.Macedo-Ribeiro, F.X.Gomis-Rüth, A.González, and M.Coll (2002).
Trypanosoma cruzi macrophage infectivity potentiator has a rotamase core and a highly exposed alpha-helix.
  EMBO Rep, 3, 88-94.
PDB code: 1jvw
11060810 B.G.Gold (2000).
Neuroimmunophilin ligands: evaluation of their therapeutic potential for the treatment of neurological disorders.
  Expert Opin Investig Drugs, 9, 2331-2342.  
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.