5T3P | pdb_00005t3p

Crystal structure of Human Peroxisomal coenzyme A diphosphatase NUDT7

• PDB DOI: https://doi.org/10.2210/pdb5T3P/pdb

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


• Deposited: 2016-08-26 Released: 2017-09-13 
• Deposition Author(s): Srikannathasan, V., Nunez, C.A., Tallant, C., Siejka, P., Mathea, S., Kopec, J., Elkins, J.M., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.225 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Human Peroxisomal coenzyme A diphosphatase NUDT7

Srikannathasan, V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.75 kDa 
• Atom Count: 5,567 
• Modeled Residue Count: 660 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal coenzyme A diphosphatase NUDT7	A, B, C	236	Homo sapiens	Mutation(s): 0  Gene Names: NUDT7 EC: 3.6.1 (PDB Primary Data), 3.6.1.77 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0C024 (Homo sapiens) Explore P0C024  Go to UniProtKB:  P0C024
PHAROS:  P0C024 GTEx:  ENSG00000140876

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.225 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.73	α = 90
b = 113.73	β = 90
c = 108.2	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Srikannathasan, V., Nunez, C.A., Tallant, C., Siejka, P., Mathea, S., Kopec, J., Elkins, J.M., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2018-02-07
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description