PDBsum entry 2z6w

Isomerase/immunosuppressant

PDB id: 2z6w

Contents

Protein chains

164 a.a. *

11 a.a. *

Ligands

CIT

Waters ×524

* Residue conservation analysis

PDB id:

2z6w

Name:

Isomerase/immunosuppressant

Title:

Crystal structure of human cyclophilin d in complex with cyclosporin a

Structure:

Peptidyl-prolyl cis-trans isomerase. Chain: a, b. Fragment: residues 2-165. Synonym: ppiase, rotamase, cyclophilin d. Engineered: yes. Mutation: yes. Cyclosporin a. Chain: m, n. Synonym: ciclosporin, ciclosporine.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ppif, cyp3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Tolypocladium inflatum. Organism_taxid: 29910

Resolution:

0.96Å R-factor: 0.130 R-free: 0.153

Authors:

K.Kajitani,M.Fujihashi,Y.Kobayashi,S.Shimizu,Y.Tsujimoto,K.Miki

Key ref:

K.Kajitani et al. (2008). Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution. Proteins, 70, 1635-1639. PubMed id: 18076075 DOI: 10.1002/prot.21855

Date:

09-Aug-07 Release date: 29-Apr-08

Protein chains

P30405  (PPIF_HUMAN) -  Peptidyl-prolyl cis-trans isomerase F, mitochondrial from Homo sapiens

Seq: 207 a.a.

Struc: 164 a.a.*

Protein chains

No UniProt id for this chain

Struc: 11 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.5.2.1.8 - peptidylprolyl isomerase.
• Reaction: [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1002/prot.21855

Proteins 70:1635-1639 (2008)

PubMed id: 18076075

Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution.

K.Kajitani, M.Fujihashi, Y.Kobayashi, S.Shimizu, Y.Tsujimoto, K.Miki.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. (A) Overall structure of CypD in complex with CsA. CypD and CsA are shown as ribbon- and stick-models, respectively. Panels A, B, and D were drawn with PyMOL (http://www.pymol.org). (B) Close-up view of CsA superimposed on its Fo-Fc omit electron density map (blue mesh) contoured at 6.0 . (C) Binding geometry of CsA on CypD. Green circles mark the CsA atoms involved in the hydrophobic contact with CypD. The CypD residues in green ellipsoids are involved in the hydrophobic interactions with CsA. The red dotted lines represent hydrogen bonding. This panel was prepared based on a scheme drawn with LIGPLOT.[21] Abbreviations of CsA residues: Bmt, (4R)-4[(E)-2-butenyl]-4,N-dimethyl-L-threonine; Aba: L- -aminobutyric acid, Sar: sarcosine, Mle, N-methyl leucine; Dal, D-alanine; Mva, N-methyl valine. (D) Distribution of the conserved residues among human cyclophilins represented on the surface of the present CypD-CsA structure. Residues conserved in all five known human cyclophilins (CypA, CypB, CypC, CypD, and CypE) are shown in red. CypD residues conserved in 3 of 4, 2 of 4, and 1 of 4 other cyclophilins are shown in orange, yellow, and green, respectively, and the unconserved CypD residues in the other four cyclophilins are shown in blue. CsA is shown as a stick model.

The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 70, 1635-1639) copyright 2008.