PDBsum entry 1d7i

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Isomerase PDB id
Protein chains
107 a.a. *
NH4 ×2
SO4 ×2
DSS ×2
Waters ×114
* Residue conservation analysis

References listed in PDB file
Key reference
Title X-Ray structures of small ligand-Fkbp complexes provide an estimate for hydrophobic interaction energies.
Authors P.Burkhard, P.Taylor, M.D.Walkinshaw.
Ref. J Mol Biol, 2000, 295, 953-962. [DOI no: 10.1006/jmbi.1999.3411]
PubMed id 10656803
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.
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.
Secondary reference #1
Title Atomic structure of the rapamycin human immunophilin fkbp-12 complex
Authors G.D.Van duyne, R.F.Standaert, S.L.Schreiber, J.Clardy.
Ref. j am chem soc, 1991, 113, 7433.
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