9TH6 | pdb_00009th6

nsp14 of SARS-CoV-2 in complex with a camelid nanobody

PDB DOI: https://doi.org/10.2210/pdb9TH6/pdb
Entry: 9TH6 supersedes: 9H01

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Lama glama
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-02 Released: 2026-02-11
Deposition Author(s): Gauffre, P., Ferron, F., Canard, B.
Funding Organization(s): European Commission, Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.290 (Depositor), 0.294 (DCC)
R-Value Work:
0.233 (Depositor)
R-Value Observed:
0.236 (Depositor)

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystallographic structure of nsp14 full length from SARS-CoV-2, stabilised by a nanobody

Gauffre, P., Gaubert, A., Ferron, F., Canard, B.

To be published.

Macromolecule Content

Total Structure Weight: 76.75 kDa
Atom Count: 4,622
Modeled Residue Count: 573
Deposited Residue Count: 679
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine-N7 methyltransferase nsp14	A	547	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 2.1.1.56 (PDB Primary Data), 3.1.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
vhh anti-nsp14 of SARS-CoV-2	B	132	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.290 (Depositor), 0.294 (DCC)
R-Value Work: 0.233 (Depositor)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.514	α = 90
b = 80.801	β = 90
c = 138.117	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing
ISOLDE	model building
BUSTER	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-11

Deposition Author(s):

This entry supersedes: 9H01

Funding Organization	Location	Grant Number
European Commission	European Union	101005077
Agence Nationale de la Recherche (ANR)	France	ANR-10-INSB-05-01

Revision History (Full details and data files)

Version 1.0: 2026-02-11
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.