4zsd

From Proteopedia

(Difference between revisions)

Revision as of 08:13, 26 June 2019

Human Cyclophilin D Complexed with an Inhibitor at room temperature

Structural highlights

4zsd is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	4j5c
Gene:	PPIF, CYP3 (HUMAN)
Activity:	Peptidylprolyl isomerase, with EC number 5.2.1.8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PPIF_HUMAN] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.^[1] ^[2]

Publication Abstract from PubMed

X-ray crystallography is an established technique for ligand screening in fragment-based drug-design projects, but the required manual handling steps - soaking crystals with ligand and the subsequent harvesting - are tedious and limit the throughput of the process. Here, an alternative approach is reported: crystallization plates are pre-coated with potential binders prior to protein crystallization and X-ray diffraction is performed directly `in situ' (or in-plate). Its performance is demonstrated on distinct and relevant therapeutic targets currently being studied for ligand screening by X-ray crystallography using either a bending-magnet beamline or a rotating-anode generator. The possibility of using DMSO stock solutions of the ligands to be coated opens up a route to screening most chemical libraries.

Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography.,Gelin M, Delfosse V, Allemand F, Hoh F, Sallaz-Damaz Y, Pirocchi M, Bourguet W, Ferrer JL, Labesse G, Guichou JF Acta Crystallogr D Biol Crystallogr. 2015 Aug 1;71(Pt 8):1777-87. doi:, 10.1107/S1399004715010342. Epub 2015 Jul 31. PMID:26249358^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Eliseev RA, Malecki J, Lester T, Zhang Y, Humphrey J, Gunter TE. Cyclophilin D interacts with Bcl2 and exerts an anti-apoptotic effect. J Biol Chem. 2009 Apr 10;284(15):9692-9. doi: 10.1074/jbc.M808750200. Epub 2009, Feb 19. PMID:19228691 doi:http://dx.doi.org/10.1074/jbc.M808750200
↑ Vaseva AV, Marchenko ND, Ji K, Tsirka SE, Holzmann S, Moll UM. p53 opens the mitochondrial permeability transition pore to trigger necrosis. Cell. 2012 Jun 22;149(7):1536-48. doi: 10.1016/j.cell.2012.05.014. PMID:22726440 doi:10.1016/j.cell.2012.05.014
↑ Gelin M, Delfosse V, Allemand F, Hoh F, Sallaz-Damaz Y, Pirocchi M, Bourguet W, Ferrer JL, Labesse G, Guichou JF. Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography. Acta Crystallogr D Biol Crystallogr. 2015 Aug 1;71(Pt 8):1777-87. doi:, 10.1107/S1399004715010342. Epub 2015 Jul 31. PMID:26249358 doi:http://dx.doi.org/10.1107/S1399004715010342

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4zsd"

@@ Line 1: / Line 1: @@
 ==Human Cyclophilin D Complexed with an Inhibitor at room temperature==
-<StructureSection load='4zsd' size='340' side='right' caption='[[4zsd]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+<StructureSection load='4zsd' size='340' side='right'caption='[[4zsd]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4zsd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZSD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4zsd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZSD FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7I6:1-(4-AMINOBENZYL)-3-[(2S)-4-(METHYLSULFANYL)-1-{(2R)-2-[2-(METHYLSULFANYL)PHENYL]PYRROLIDIN-1-YL}-1-OXOBUTAN-2-YL]UREA'>7I6</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4j5c|4j5c]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4zsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zsd OCA], [http://pdbe.org/4zsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zsd RCSB], [http://www.ebi.ac.uk/pdbsum/4zsd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zsd ProSAT]</span></td></tr>
@@ Line 22: / Line 23: @@
 ==See Also==
-*[[Cyclophilin|Cyclophilin]]
+*[[Cyclophilin 3D structures|Cyclophilin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Peptidylprolyl isomerase]]
 [[Category: Allemand, F]]

4zsd

From Proteopedia

Revision as of 08:13, 26 June 2019

Human Cyclophilin D Complexed with an Inhibitor at room temperature

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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