9DFW

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

PDB DOI: https://doi.org/10.2210/pdb9DFW/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Trichoderma virens Gv29-8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-08-30 Released: 2025-02-12
Deposition Author(s): Lachowicz, J.C., Bonanno, J.B., Grove, T.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 ?
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

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.

Macromolecule Content

Total Structure Weight: 113.45 kDa
Atom Count: 7,953
Modelled Residue Count: 861
Deposited Residue Count: 951
Unique protein chains: 1

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	A, B, C	317	Trichoderma virens Gv29-8	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G9MQB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP (Subject of Investigation/LOI) Query on CTP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C]	F [auth A], M [auth B], P [auth C]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain P [auth C]
SAM (Subject of Investigation/LOI) Query on SAM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C]	E [auth A], L [auth B], O [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain O [auth C]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C]	D [auth A], K [auth B], N [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain N [auth C]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth C]	I [auth A], J [auth A], R [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth C]