9UMI | pdb_00009umi

Crystal structure of the SARS-CoV-2 spike protein HR1 in complex with a designed peptide inhibitor dP-S2FI-22 at 1.95 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb9UMI/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): synthetic construct, Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-22 Released: 2026-11-04
Deposition Author(s): Wang, K., Chen, J., Dong, Y., Ye, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.215 (Depositor), 0.216 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the SARS-CoV-2 spike protein HR1 in complex with a designed peptide inhibitor dP-S2FI-22 at 1.95 angstrom resolution

Wang, K., Chen, J., Dong, Y., Ye, S.

To be published.

Macromolecule Content

Total Structure Weight: 38.31 kDa
Atom Count: 2,976
Modeled Residue Count: 328
Deposited Residue Count: 363
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dP-S2FI-22 peptide,Spike protein S2'	A, B [auth C], C [auth E]	121	synthetic construct, Severe acute respiratory syndrome coronavirus 2 This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.252 (Depositor), 0.250 (DCC)
R-Value Work: 0.215 (Depositor), 0.216 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.003	α = 90
b = 42.223	β = 106.891
c = 67.3	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release