5CBT | pdb_00005cbt

Human Cyclophilin D Complexed with Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5CBT/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-01 Released: 2016-07-20 
• Deposition Author(s): Gibson, R.P., Shore, E., Kershaw, N., Awais, M., Javed, A., Latawiec, D., Pandalaneni, S., Wen, L., Berry, N., O'Neill, P., Sutton, R., Lian, L.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.199 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Human Cyclophilin D Complexed with Inhibitor

Gibson, R.P., Shore, E., Kershaw, N., Awais, M., Javed, A., Latawiec, D., Pandalaneni, S., Wen, L., Berry, N., O'Neill, P., Sutton, R., Lian, L.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.55 kDa 
• Atom Count: 1,412 
• Modeled Residue Count: 164 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A	165	Homo sapiens	Mutation(s): 0  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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4ZL	B [auth A]	ethyl N-(benzylcarbamoyl)glycinate C12 H16 N2 O3 JOGHOEBNQXZSDF-UHFFFAOYSA-N
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	H [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.199 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.849	α = 90
b = 57.849	β = 90
c = 114.455	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Gibson, R.P., Shore, E., Kershaw, N., Awais, M., Javed, A., Latawiec, D., Pandalaneni, S., Wen, L., Berry, N., O'Neill, P., Sutton, R., Lian, L.Y.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description