9DFN

X-ray crystal structure of the second viperin-like enzyme from Trichoderma virens with bound CTP and SAM

• PDB DOI: https://doi.org/10.2210/pdb9DFN/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Trichoderma virens Gv29-8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-30 Released: 2025-02-19 
• Deposition Author(s): Lachowicz, J.C., Grove, T.G., Bonanno, J.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.197 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.65 kDa 
• Atom Count: 2,766 
• Modelled Residue Count: 283 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Radical SAM core domain-containing protein	A	321	Trichoderma virens Gv29-8	Mutation(s): 0  Gene Names: TRIVIDRAFT_46896
UniProt
Find proteins for G9N0G3 (Hypocrea virens (strain Gv29-8 / FGSC 10586)) Explore G9N0G3  Go to UniProtKB:  G9N0G3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTP (Subject of Investigation/LOI)	D [auth A]	CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N
SAM (Subject of Investigation/LOI)	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4 (Subject of Investigation/LOI)	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.197 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.808	α = 90
b = 57.838	β = 90
c = 157.692	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Lachowicz, J.C., Grove, T.G., Bonanno, J.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM007491

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release