33VD | pdb_000033vd

SAD-phased structure of SARS-CoV-2 Nucleocapsid protein CTD.

PDB DOI: https://doi.org/10.2210/pdb33VD/pdb

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

Deposited: 2026-08-25 Released: 2026-09-09
Deposition Author(s): Koekemoer, L., Duman, R., Liu, H., Aschenbrenner, J.C., Von Delft, F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free:
0.174 (Depositor), 0.175 (DCC)
R-Value Work:
0.148 (Depositor), 0.148 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 33VD

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

Literature

SAD-phased structure of SARS-CoV-2 Nucleocapsid protein CTD.

Koekemoer, L., Duman, R., Aschenbrenner, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 36.98 kDa
Atom Count: 3,077
Modeled Residue Count: 334
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	169	Severe acute respiratory syndrome coronavirus	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.2.2 (PDB Primary Data), 3.4.19.12 (PDB Primary Data), 3.4.22 (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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free: 0.174 (Depositor), 0.175 (DCC)
R-Value Work: 0.148 (Depositor), 0.148 (DCC)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.5	α = 90
b = 88.5	β = 90
c = 39.4	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
XDS	data reduction
gemmi	data extraction
REFMAC	refinement
CRANK2	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Aschenbrenner, J.C.

Funding Organization	Location	Grant Number
Other government	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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