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)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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