PDBsum entry 1bl4

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
Protein chains
107 a.a. *
AP1 ×2
Waters ×69
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Fkbp mutant f36v complexed with remodeled synthetic ligand
Structure: Protein (fk506 binding protein). Chain: a, b. Synonym: fkbp. Engineered: yes. Mutation: yes. Other_details: complexed with redesigned compound
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
1.90Å     R-factor:   0.188     R-free:   0.230
Authors: M.H.Hatada,T.Clackson,W.Yang,L.W.Rozamus,J.Amara, C.T.Rollins,L.F.Stevenson,S.R.Magari,S.A.Wood,N.L.Courage, X.Lu,F.Cerasoli Junior,M.Gilman,D.Holt
Key ref:
T.Clackson et al. (1998). Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity. Proc Natl Acad Sci U S A, 95, 10437-10442. PubMed id: 9724721 DOI: 10.1073/pnas.95.18.10437
23-Jul-98     Release date:   02-Sep-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P62942  (FKB1A_HUMAN) -  Peptidyl-prolyl cis-trans isomerase FKBP1A
108 a.a.
107 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - 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: 10.1073/pnas.95.18.10437 Proc Natl Acad Sci U S A 95:10437-10442 (1998)
PubMed id: 9724721  
Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity.
T.Clackson, W.Yang, L.W.Rozamus, M.Hatada, J.F.Amara, C.T.Rollins, L.F.Stevenson, S.R.Magari, S.A.Wood, N.L.Courage, X.Lu, F.Cerasoli, M.Gilman, D.A.Holt.
FKBP ligand homodimers can be used to activate signaling events inside cells and animals that have been engineered to express fusions between appropriate signaling domains and FKBP. However, use of these dimerizers in vivo is potentially limited by ligand binding to endogenous FKBP. We have designed ligands that bind specifically to a mutated FKBP over the wild-type protein by remodeling an FKBP-ligand interface to introduce a specificity binding pocket. A compound bearing an ethyl substituent in place of a carbonyl group exhibited sub-nanomolar affinity and 1,000-fold selectivity for a mutant FKBP with a compensating truncation of a phenylalanine residue. Structural and functional analysis of the new pocket showed that recognition is surprisingly relaxed, with the modified ligand only partially filling the engineered cavity. We incorporated the specificity pocket into a fusion protein containing FKBP and the intracellular domain of the Fas receptor. Cells expressing this modified chimeric protein potently underwent apoptosis in response to AP1903, a homodimer of the modified ligand, both in culture and when implanted into mice. Remodeled dimerizers such as AP1903 are ideal reagents for controlling the activities of cells that have been modified by gene therapy procedures, without interference from endogenous FKBP.
  Selected figure(s)  
Figure 1.
Fig. 1. (A) Chemical structure of synthetic FKBP ligand 1, with the -keto-pipecolylamide core region colored red. The arrow indicates the C9 carbonyl position modified in this study. A carboxylate group (Right) was included in all ligands to facilitate subsequent engineering of dimers. (B) Portion of the x-ray crystal structure of the complex between human FKBP12 and a synthetic compound related to 1 (from ref. 2). Only the -keto-pipecolylamide core of the compound is shown, corresponding to the region colored red in Fig. 1A.
Figure 2.
Fig. 2. X-ray crystal structure of the 5S-F36V-FKBP complex. (A) Overview of the complex. (B) Sidechains contacting the ethyl bump of 5S. Side chains are shown in gray, and main chain is shown in brown. The van der Waals surface of the ethyl bump of 5S is shown (yellow dots). (C) A section through the ligand binding site of the complex showing the large cavity created by the F36V mutation. (D) Equivalent section through the complex between the wild-type protein and an unbumped compound related to 1, shown in white (2). For comparison, the Val36 side chain and the 5S core region from C are overlaid (yellow), based on a superposition of the main chain atoms in the two structures.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB code: 1eym
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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.