The Protein Folding Database
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  Statistics
Version: 2.2
Last Update: 8-Jun-2007
Entries: 296
Proteins: 70
Families: 53
Species: 30
ϕ values: 230 (5 proteins)
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  Latest Additions
ACBP (3 WT)
FRB (6 WT)
CI2 (3 WT, 202 mutants)
HPr (1 WT, 4 mutants)
Im7 (1 WT)
En-HD (1 WT)
Im9 (2 WT)
Abp1 SH3 (1 WT)
CheW (1 WT)
U1A (1 WT)
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Fulton et al (2005) Nucleic Acids Res. 33:D279-283  |  Fulton et al (2007) Nucleic Acids Res. 35:D304-307 About PFD | Help | Glossary

Folding Data
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Note: A field with its data listed as "ND" denotes there is no data for that field.
[Measurement ID: 214] contact us to make corrections & updates to this data

Expand   Compare Data
compare with other measurements for this constructcompare with other measurements for this protein (44)compare with other measurements for proteins in this SCOP Family (44)

Expand   Protein Data
Protein Name FK-506 binding protein (FKBP12)   -  mutant: FKBP12
Oligomeric State Monomer
Folding Mechanism Nucleation-condensation
Intermediates 0
Phi Pattern CI2
SCOP Class Alpha+Beta   |   goto SCOP
SCOP Family FKBP immunophilin/proline isomerase   |   goto SCOP

Expand   Construct Data
Species Human (Homo sapiens)

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Sequence GSMGVQVETISPGDGRTFPKRGGTCVVHTGMLQDGKKFDSSRDRNKPFKF
MLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLV
FDVELLKLE

Blast PFD  |  Blast NCBI NR
Length 110
Molecular Weight 11841.6Da
Fusion None
PDB ID 1FKB   |   goto PDB  
PDB Resolution 1.7Å
Chain Any chain
Residues 1 - 107
SCOP ID 54537   |   goto SCOP
UniProt ID FKB1A_HUMAN   |   goto UniProt
Relative Contact Order 16.91

Expand   Publication Data
Publication Main ERG et al (1998) Context-Dependent Nature of Destabilizing Mutations on the Stability of FKBP12, Biochemistry 37, 6145-6153  goto pubmed
Data type in publication Equilibrium
Publication Fulton KF et al (1999) Mapping the interactions present in the transition state for unfolding/folding of FKBP12, J. Mol. Biol. 291, 445-461  goto pubmed
Data type in publication Kinetic

Expand   Graphical Analysis Data
Contact Order Plot Data Acyl Coenzyme A Binding Protein Hypothetical protein YjbJ from Escherichia coli E colicin binding Immunity Protein 7 (ImmE7*) E colicin binding Immunity Protein 9 (ImmE9) Lambda C1 repressor, DNA-binding domain E colicin binding Immunity Protein 9 (ImmE9) Acyl Coenzyme A Binding Protein Acyl Coenzyme A Binding Protein Internalin B, C-terminal domain Apo-azurin Chemotaxis protein CheW Fyn proto-oncogene tyrosine kinase, SH3 domain Alpha-Spectrin SH3 Domain c-src tyrosine kinase SH3 Domain Actin binding protein 1 SH3 domain Activation Domain Of Human Procarboxypeptidase A2 Chymotrypsin Inhibitor 2 Ribosomal protein L9 C-domain FK-506 binding protein Ribosomal protein L23 Acylphosphatase Ribosomal protein L9 N-domain Immunoglobulin-binding protein G Immunoglobulin light chain-binding domain of protein L c-Raf1 RBD Ribosomal protein S6 c-src tyrosine kinase SH2 domain Spliceosomal U1A protein Ubiquitin FK-506 binding protein Chymotrypsin Inhibitor 2 Chymotrypsin Inhibitor 2
generated contact order graph

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Clicking on a data point will display folding data on that protein.
To view more data on a SCOP Class click on it's name in the legend.
Note: Mutant measurements do not have their data plotted on this graph, instead the data from wildtype is marked in red.

view notes on contact order

Expand   Equilibrium Data & Methods
Equilibrium Data
[Denaturant] Minimum
(M)		 [Denaturant] 50%
(M)		 mD-N (m)
(kJ mol-1 M-1)		 mD-N <m>
(kJ mol-1 M-1)		 ∆GD-N (m)
(kJ mol-1)		 ∆GD-N <m>
(kJ mol-1)
ND 3.87 ± 0.02 5.98 ± 0.21 6.64 ± 0.07 23.13 ± 0.82 25.69 ± 0.3
Probe Trp Fluorescence  what is this?
Pertubation Denaturant  what is this?
Technique Urea
Instrument Perkin-Elmer LS50B Luminescence Spectrometer
Temperature 298K
pH 7.5
Buffer 0.05M TrisHCl
Additive 1: 0.0010M DTT
Protein Concentration 0.0020M

Expand   Kinetic Data & Methods
Kinetic Unfolding Data
[Denaturant] Minimum
(M)		 [Denaturant] Maximum
(M)		 ku
(s-1)		 lnku
(s-1)		 mu
(M-1)		 m‡-N
(kJ mol-1 M-1)
5.5 8.5 0.0002120 ± 0.0000010 (0M) -8.46 ± 0.11 (0M) 0.9 ± 0.02 2.23 ± 0.05
Kinetic Folding Data
[Denaturant] Minimum
(M)		 [Denaturant] Maximum
(M)		 kfH2O
(s-1)		 ln(kfH2O)
(s-1)		 mf
(M-1)		 m‡-D
(kJ mol-1 M-1)
ND 3.5 4.2631 ± 0.0077 1.45 ± 0.06 -1.85 ± 0.05 -4.58 ± 0.12
Other Kinetic Data
[Denaturant] 50%
(M)		 KD-N mD-N ∆GD-NH2O Kinetic βT Kinetic Unfolding βT Kinetic Folding βT Equilibrium Unfolding βT Equilibrium Folding
ND ND 6.81 ± 0.13 ND 0.67 ± 0.01 0.67 ± 0.02 0.63 ± 0.02 0.77 ± 0.03
Probe Trp Fluorescence  what is this?
Pertubation Denaturant  what is this?
Technique Urea
Instrument Applied Photophysics SF.17MV Stopped-flow Spectrophotometer
Temperature 298K
pH 7.5
Buffer 0.05M TrisHCl
Additive 1: 0.0010M DTT
Protein Concentration 0.0020M
Unfolding Fit Linear
Refolding Fit Linear

Expand   Mutant Data
Mutation Name FKBP12
Mutation Type
Contacts
Location
Secondary Structure
Local Interactions
Asa ND
Buried Asa ND
PDB 1FKB

Expand   Notes & Comments on this measurement
Measurement Notes
Protein Notes FK-506 binding protein (FKBP12), an immunophilin. It contains no disulphide bridges, and all of its seven proline residues are in a trans conformation in the native state, thus the folding will not be limited by disulphide bond formation or rearrangement, or proline isomerisation. In addition, it has been shown that FKBP12 undergoes a reversible twostate unfolding under equilibrium conditions which can be induced using urea or guanidinium chloride (GdnHCl). The structure of FKBP12 is characterised by a large, amphiphilic, antiparallel 5-stranded beta-sheet with +3, +1, -3, -1 topology. An amphiphilic alpha-helix packs against the hydrophobic face of the beta-sheet at an angle of 60 degrees with respect to the long axis. The beta-sheet has a righthanded twist and wraps around the helix to form a well-ordered hydrophobic core. The immunosuppressant- binding site, which contains many aromatic side-chains, forms a large, shallow hydrophobic pocket between the alpha-helix and beta-sheet. A notable feature of FKBP12 resulting from the +3, +1, -3, -1 topology of the beta-sheet is a topological crossing of loop-1(Pro9-Gln20 which connects beta-strand 1 and beta-strand 2), and loop-4 (Ala64-Gln70 which connects the alpha-helix to beta-strand 4). Although crossing topologies have been observed in proteins containing parallel beta-sheets, they are rare in antiparallel beta-sheet structures. It has been suggested that the topological crossing of loops may result in complex folding pathways which would slow folding, and may even result in misfolded species which would form kinetic traps on the folding pathway.
Construct Notes
Mutant Notes
Equilibrium Notes SLM Aminico Bowman series 2 instrument was used for some mutants.
Kinetic Notes Unfolding experiments for some mutants were performed using a manual mixing Perkin-Elmer MPF-44B fluorescence spectrophotometer.
Comments view comments on this measurement

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