5NKS | pdb_00005nks

Human Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4)

• PDB DOI: https://doi.org/10.2210/pdb5NKS/pdb

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


• Deposited: 2017-03-31 Released: 2017-11-01 
• Deposition Author(s): Mathea, S., Elkins, J.M., Strain-Damerell, C., Salah, E., Borkowska, O., Chalk, R., Burgess-Brown, N., Pinkas, D.M., von Delft, F., Krojer, T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Human Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4)

Mathea, S., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 62.04 kDa 
• Atom Count: 4,057 
• Modeled Residue Count: 490 
• Deposited Residue Count: 573 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropyrimidinase-related protein 4	A	573	Homo sapiens	Mutation(s): 0  Gene Names: DPYSL4, CRMP3, ULIP4
UniProt & NIH Common Fund Data Resources
Find proteins for O14531 (Homo sapiens) Explore O14531  Go to UniProtKB:  O14531
PHAROS:  O14531 GTEx:  ENSG00000151640

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.47	α = 90
b = 102.65	β = 90
c = 116.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Mathea, S., Elkins, J.M., Strain-Damerell, C., Salah, E., Borkowska, O., Chalk, R., Burgess-Brown, N., Pinkas, D.M., von Delft, F., Krojer, T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description