7ZOM | pdb_00007zom

Crystal structure of N-terminal catalytic domain of human PLAAT3

• PDB DOI: https://doi.org/10.2210/pdb7ZOM/pdb

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


• Deposited: 2022-04-26 Released: 2023-04-26 
• Deposition Author(s): von Castelmur, E., Perrakis, A.
• Funding Organization(s): Swiss National Science Foundation, Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 

Literature

Crystal structure of N-terminal catalytic domain of human PLAAT3

von Castelmur, E., Perrakis, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 15.18 kDa 
• Atom Count: 990 
• Modeled Residue Count: 105 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A and acyltransferase 3	A	132	Homo sapiens	Mutation(s): 0  Gene Names: PLAAT3, HRASLS3, HREV107, PLA2G16 EC: 2.3.1 (PDB Primary Data), 3.1.1.32 (PDB Primary Data), 3.1.1.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P53816 (Homo sapiens) Explore P53816  Go to UniProtKB:  P53816
PHAROS:  P53816 GTEx:  ENSG00000176485

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A], C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.638	α = 90
b = 60.638	β = 90
c = 74.069	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): von Castelmur, E., Perrakis, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--
Netherlands Organisation for Scientific Research (NWO)	Netherlands	--

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection