3GRO

Human palmitoyl-protein thioesterase 1

• PDB DOI: https://doi.org/10.2210/pdb3GRO/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2009-03-26 Released: 2009-04-07 
• Deposition Author(s): Dobrovetsky, E., Seitova, A., Tong, Y., Tempel, W., Dong, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Cossar, D., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.238 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Human palmitoyl-protein thioesterase 1

Dobrovetsky, E., Seitova, A., Tong, Y., Tempel, W., Dong, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Cossar, D., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.29 kDa 
• Atom Count: 4,263 
• Modelled Residue Count: 552 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Palmitoyl-protein thioesterase 1	A, B	298	Homo sapiens	Mutation(s): 0  Gene Names: PPT1, PPT EC: 3.1.2.22 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P50897 (Homo sapiens) Explore P50897  Go to UniProtKB:  P50897
PHAROS:  P50897 GTEx:  ENSG00000131238

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	C [auth A], D [auth A], E [auth B], F [auth B]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.238 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.71	α = 90
b = 90.642	β = 90
c = 129.165	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-3000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Dobrovetsky, E., Seitova, A., Tong, Y., Tempel, W., Dong, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Cossar, D., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-11-06
  Changes: Structure summary