5ROB

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 helicase

PDB DOI: https://doi.org/10.2210/pdb5ROB/pdb
Deposition Group: G_1002166 (ground state) ExploreG_1002166

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

Deposited: 2020-09-22 Released: 2021-03-10
Deposition Author(s): Newman, J.A., Yosaatmadja, Y., Douangamath, A., Aimon, A., Powell, A.J., Dias, A., Fearon, D., Dunnett, L., Brandao-Neto, J., Krojer, T., Skyner, R., Gorrie-Stone, T., Thompson, W., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.254
R-Value Work: 0.219
R-Value Observed: 0.221

wwPDB Validation 3D Report Full Report

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

Literature

PanDDA analysis group deposition of ground-state model

Newman, J.A., Yosaatmadja, Y., Douangamath, A., Aimon, A., Powell, A.J., Dias, A., Fearon, D., Dunnett, L., Brandao-Neto, J., Krojer, T., Skyner, R., Gorrie-Stone, T., Thompson, W., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 134.63 kDa
Atom Count: 9,407
Modelled Residue Count: 1,157
Deposited Residue Count: 1,202
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase	A [auth B], B [auth A]	601	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	F [auth B], G [auth B], K [auth A], L [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain K [auth A] Focus chain L [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	C [auth B] D [auth B] E [auth B] H [auth A] I [auth A] C [auth B], D [auth B], E [auth B], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]