3EBQ | pdb_00003ebq

Crystal structure of human PPPDE1

• PDB DOI: https://doi.org/10.2210/pdb3EBQ/pdb

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


• Deposited: 2008-08-28 Released: 2008-11-04 
• Deposition Author(s): Walker, J.R., Akutsu, M., Qiu, L., Li, Y., Slessarev, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Botchkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Structure of Human PPPDE1

Walker, J.R., Akutsu, M., Qiu, L., Li, Y., Slessarev, Y., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.82 kDa 
• Atom Count: 1,190 
• Modeled Residue Count: 144 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MOLECULE: PPPDE1 (PERMUTED PAPAIN FOLD PEPTIDASES OF DSRNA VIRUSES AND EUKARYOTES 1), UPF0326 protein FAM152B	A	170	Homo sapiens	Mutation(s): 0  Gene Names: FAM152B EC: 3.4.22 (PDB Primary Data), 3.4 (UniProt), 3.1.2.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ICB0 (Homo sapiens) Explore Q6ICB0  Go to UniProtKB:  Q6ICB0
PHAROS:  Q6ICB0 GTEx:  ENSG00000100418

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	B [auth A], C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.625	α = 90
b = 41.625	β = 90
c = 184.239	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Walker, J.R., Akutsu, M., Qiu, L., Li, Y., Slessarev, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Botchkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations