8UC5

Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)

• PDB DOI: https://doi.org/10.2210/pdb8UC5/pdb

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


• Deposited: 2023-09-25 Released: 2024-09-04 
• Deposition Author(s): Kreitler, D.F., Rangwala, A.M., Seeliger, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.175 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Starting Model: experimental

Literature

Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)

Kreitler, D.F., Seeliger, M.A., Rangwala, A.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54.61 kDa 
• Atom Count: 4,190 
• Modelled Residue Count: 495 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A [auth X], B [auth A], C [auth B]	166	Homo sapiens	Mutation(s): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X], M [auth A], N [auth A], O [auth A], R [auth B], S [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	K [auth X], L [auth X], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	J [auth X], P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.175 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.667	α = 90
b = 56.643	β = 123.72
c = 101.172	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIMPLE	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Kreitler, D.F., Rangwala, A.M., Seeliger, M.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM119437
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	F30CA260771

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release