3KVH

Crystal structure of human protein syndesmos (NUDT16-like protein)

• PDB DOI: https://doi.org/10.2210/pdb3KVH/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-30 Released: 2010-01-19 
• Deposition Author(s): Tresaugues, L., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Kotzsch, A., Kraulis, P., Moche, M., Nielsen, T.K., Nyman, T., Persson, C., Roos, A.K., Schuler, H., Schutz, P., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.217 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Crystal structure of human protein syndesmos (NUDT16L1)

Tresaugues, L., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Kotzsch, A., Kraulis, P., Moche, M., Nielsen, T.K., Nyman, T., Persson, C., Roos, A.K., Schuler, H., Schutz, P., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 24.07 kDa 
• Atom Count: 1,713 
• Modelled Residue Count: 192 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein syndesmos	A	214	Homo sapiens	Mutation(s): 0  Gene Names: NUDT16L1, SDOS
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRJ7 (Homo sapiens) Explore Q9BRJ7  Go to UniProtKB:  Q9BRJ7
GTEx:  ENSG00000168101

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.217 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.811	α = 90
b = 60.278	β = 118.64
c = 60.483	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Tresaugues, L., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Kotzsch, A., Kraulis, P., Moche, M., Nielsen, T.K., Nyman, T., Persson, C., Roos, A.K., Schuler, H., Schutz, P., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description