5NWO

Human Cyclophilin D Complexed with Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Human Cyclophilin D Complexed with Inhibitor

Zacharchenko, T.Lian, L.Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase F, mitochondrial
A
165Homo sapiensMutation(s): 0 
Gene Names: PPIF (CYP3)
EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens)
Go to Gene View: PPIF
Go to UniProtKB:  P30405
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
12P
Query on 12P

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Download CCD File 
A
DODECAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
 Ligand Interaction
9CK
Query on 9CK

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Download CCD File 
A
1-[(4-aminophenyl)methyl]-3-[2-[2-(2-bromophenyl)pyrazolidin-1-yl]-2-oxidanylidene-ethyl]urea
C19 H22 Br N5 O2
CDUGYVAEBXUUHW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.450α = 90.00
b = 57.450β = 90.00
c = 114.910γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release