7ZDN

Human Cyclophilin D in complex with fragment

• PDB DOI: https://doi.org/10.2210/pdb7ZDN/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2022-03-29 Released: 2023-04-19 
• Deposition Author(s): Silva, D.O., Graedler, U., Bandeiras, T.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7PMT 7R2H 7R2I

Literature

Human Cyclophilin D in complex with fragment

Silva, D.O., Graedler, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.95 kDa 
• Atom Count: 2,963 
• Modelled Residue Count: 328 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A, B	165	Homo sapiens	Mutation(s): 2  Gene Names: PPIF, CYP3 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens) Explore P30405  Go to UniProtKB:  P30405
PHAROS:  P30405 GTEx:  ENSG00000108179

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IU0 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(1~{R},9~{R},10~{S})-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-10-ol C11 H13 N O2 JEDSYLJTJIINOF-GMTAPVOTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.412	α = 90
b = 81.877	β = 90
c = 113.395	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Silva, D.O., Graedler, U., Bandeiras, T.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description