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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.238 (Depositor), 0.250 (DCC)
R-Value Work:
0.200 (Depositor), 0.220 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50897
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.250 (DCC)
R-Value Work: 0.200 (Depositor), 0.220 (DCC)
R-Value Observed: 0.202 (Depositor)

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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