13UD | pdb_000013ud

Orf9b homodimer in complex with fragment ZINC000000404753

PDB DOI: https://doi.org/10.2210/pdb13UD/pdb
Deposition Group: G_1002357 | Explore G_1002357

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-19 Released: 2026-08-26
Deposition Author(s): San Felipe, C.J., Fraser, J.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.244 (Depositor), 0.244 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 13UD

Ligand Structure Quality Assessment

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

Literature

Orf9b homodimer in complex with fragments

San Felipe, C.J., Fraser, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 22.02 kDa
Atom Count: 1,343
Modeled Residue Count: 162
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF9b protein	A, B	97	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: 9b
UniProt
Find proteins for P0DTD2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD2 Go to UniProtKB: P0DTD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BRB (Subject of Investigation/LOI) Query on BRB Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	PARA-BROMOBENZYL ALCOHOL C₇ H₇ Br O VEDDBHYQWFOITD-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.244 (Depositor), 0.244 (DCC)
R-Value Work: 0.215 (Depositor), 0.215 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.832	α = 90
b = 64.894	β = 90
c = 73.525	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

San Felipe, C.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171110

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.