6B09

Crystal structure of HsNUDT16 in complex with diADPR (soaked)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(AD-ribosyl)ated proteins

Thirawatananond, P.McPherson, R.L.Malhi, J.Nathan, S.Lambrecht, M.Brichacek, M.Hergenrother, P.Leung, A.Gabelli, S.B.

(2019) Sci Rep --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U8 snoRNA-decapping enzyme
A, B
195Homo sapiensMutation(s): 1 
Gene Names: NUDT16
EC: 3.6.1.62
Find proteins for Q96DE0 (Homo sapiens)
Go to Gene View: NUDT16
Go to UniProtKB:  Q96DE0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
C7G
Query on C7G

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A, B
[(2~{R},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{S},4~{S},5~{S})-5-[[[[(2~{R},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate
DIADPR
C25 H36 N10 O23 P4
CSEMRHUJDKFXPV-OATIKAJMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.256 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.395α = 90.00
b = 47.063β = 108.74
c = 75.792γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
Cootmodel building
StructureStudiodata collection
HKL-3000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release