5SM2 | pdb_00005sm2

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z3006151474

PDB DOI: https://doi.org/10.2210/pdb5SM2/pdb
Deposition Group: G_1002230 (changed state) ExploreG_1002230

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-03 Released: 2022-03-16
Deposition Author(s): Imprachim, N., Yosaatmadja, Y., von-Delft, F., Bountra, C., Gileadi, O., Newman, J.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.270 (Depositor), 0.260 (DCC)
R-Value Work:
0.250 (Depositor), 0.230 (DCC)
R-Value Observed:
0.251 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

PanDDA analysis group deposition

Imprachim, N., Yosaatmadja, Y., von-Delft, F., Bountra, C., Gileadi, O., Newman, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 60.24 kDa
Atom Count: 4,138
Modeled Residue Count: 459
Deposited Residue Count: 523
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proofreading exoribonuclease nsp14	A [auth D]	523	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.1.13
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LQ3 (Subject of Investigation/LOI) Query on LQ3 Download Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain H [auth D] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] mmCIF format, chain G [auth D] mmCIF format, chain H [auth D]	G [auth D], H [auth D]	(5S)-5-(difluoromethoxy)pyridin-2(5H)-one C₆ H₅ F₂ N O₂ LTVXNUWMTTYHRL-BYPYZUCNSA-N		Interactions Focus chain G [auth D] Focus chain H [auth D] Interactions & Density Focus chain G [auth D] Focus chain H [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain F [auth D] MOL2 format, chain E [auth D] MOL2 format, chain F [auth D] mmCIF format, chain E [auth D] mmCIF format, chain F [auth D]	E [auth D], F [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth D] Focus chain F [auth D] Interactions & Density Focus chain E [auth D] Focus chain F [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth D] SDF format, chain C [auth D] SDF format, chain D MOL2 format, chain B [auth D] MOL2 format, chain C [auth D] MOL2 format, chain D mmCIF format, chain B [auth D] mmCIF format, chain C [auth D] mmCIF format, chain D	B [auth D], C [auth D], D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth D] Focus chain C [auth D] Focus chain D Interactions & Density Focus chain B [auth D] Focus chain C [auth D] Focus chain D