8UC4 | pdb_00008uc4

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

• PDB DOI: https://doi.org/10.2210/pdb8UC4/pdb

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


• Deposited: 2023-09-25 Released: 2024-08-07 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

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.

Macromolecule Content 

• Total Structure Weight: 21.16 kDa 
• Atom Count: 1,401 
• Modeled Residue Count: 164 
• Deposited Residue Count: 166 
• 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]	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
15P	B [auth X], E [auth X]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N
PEG	C [auth X], D [auth X]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	F [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.959	α = 90
b = 56.959	β = 90
c = 109.781	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Kreitler, D.F., Rangwala, A.M., Seeliger, M.A.

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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: 2024-08-07
  Type: Initial release