5CBV

Human Cyclophilin D Complexed with Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5CBV/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• 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: 1.80 Å
• R-Value Free: 0.192 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.53 kDa 
• Atom Count: 1,424 
• Modelled Residue Count: 164 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Cyclophilin D	A	165	Homo sapiens	Mutation(s): 1
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4ZP	F [auth A]	ethyl N-{[3-(pyridin-3-yl)benzyl]carbamoyl}glycinate C17 H19 N3 O3 MLAVNVQEXCHEOH-UHFFFAOYSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.192 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.43	α = 90
b = 57.43	β = 90
c = 113.04	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, Refinement description