Download MendeleyStructural 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.
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
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- 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
View more details
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Radical SAM core domain-containing protein | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | G9N0G3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CTP (Subject of Investigation/LOI) Query on CTP | D [auth A] | CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N |  | ||
| SAM (Subject of Investigation/LOI) Query on SAM | C [auth A] | S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N |  | ||
| SF4 (Subject of Investigation/LOI) Query on SF4 | B [auth A] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- 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 ( ? ) | Angle ( ? ) |
|---|---|
| a = 36.808 | α = 90 |
| b = 57.838 | β = 90 |
| c = 157.692 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-02-19 Deposition Author(s): Lachowicz, J.C., Grove, T.G., Bonanno, J.B.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM007491 |
Revision History (Full details and data files)
- Version 1.0: 2025-02-19
Type: Initial release
