9DFW

X-ray crystal structure of an engineered Viperin-like enzyme from T. virens with bound CTP and SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.188 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CTPClick on this verticalbar to view detailsBest fitted SAMClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Structural Insights from Active Site Variants and B-8 Loop Interactions in Viperin-like Enzymes

Lachowicz, J.C.Grudman, S.Bonanno, J.B.Fiser, A.Grove, T.L.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Radical SAM core domain-containing protein
A, B, C
317Trichoderma virens Gv29-8Mutation(s): 7 
Gene Names: TRIVIDRAFT_58105
UniProt
Find proteins for G9MQB8 (Hypocrea virens (strain Gv29-8 / FGSC 10586))
Explore G9MQB8 
Go to UniProtKB:  G9MQB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9MQB8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CTP (Subject of Investigation/LOI)
Query on CTP

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
P [auth C]
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
O [auth C]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
N [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
Q [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
R [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.188 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.131α = 90
b = 85.131β = 90
c = 110.471γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CTPClick on this verticalbar to view detailsBest fitted SAMClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM007491

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release