9Z1F | pdb_00009z1f

Crystal structure of NJ receptor binding domain in complex with human ACE2

PDB DOI: https://doi.org/10.2210/pdb9Z1F/pdb

Classification: IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Spodoptera frugiperda, Homo sapiens
Mutation(s): No

Deposited: 2025-11-04 Released: 2026-11-11
Deposition Author(s): Feng, Z., Wilson, I.A.
Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.219 (Depositor), 0.219 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of NJ RBDs

Feng, Z., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 191.84 kDa
Atom Count: 13,349
Modeled Residue Count: 1,577
Deposited Residue Count: 1,600
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NJ spike protein S1	A [auth N], B [auth A]	203	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth N] Focus chain B [auth A]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	C [auth B], D [auth E]	597	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain C [auth B] Focus chain D [auth E]	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth M]	6		N-Glycosylation	Interactions Focus chain E [auth M] Interactions & Density Focus chain E [auth M]

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth C]	7		N-Glycosylation	Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D], H [auth F], I [auth H], J [auth G], K [auth I], G [auth D], H [auth F], I [auth H], J [auth G], K [auth I], L [auth J], M [auth K]	2		N-Glycosylation	Interactions Focus chain G [auth D] Focus chain H [auth F] Focus chain I [auth H] Focus chain J [auth G] Focus chain K [auth I] Focus chain L [auth J] Focus chain M [auth K] Interactions & Density Focus chain G [auth D] Focus chain H [auth F] Focus chain I [auth H] Focus chain J [auth G] Focus chain K [auth I] Focus chain L [auth J] Focus chain M [auth K]

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N [auth L]	3		N-Glycosylation	Interactions Focus chain N [auth L] Interactions & Density Focus chain N [auth L]

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	P [auth B], Q [auth B], Y [auth E], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth E] Focus chain Z [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain U [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain U [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain U [auth E]	S [auth E] T [auth E] U [auth E] V [auth E] W [auth E] S [auth E], T [auth E], U [auth E], V [auth E], W [auth E], X [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain R [auth E] MOL2 format, chain O [auth B] MOL2 format, chain R [auth E] mmCIF format, chain O [auth B] mmCIF format, chain R [auth E]	O [auth B], R [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain R [auth E] Interactions & Density Focus chain O [auth B] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.264 (Depositor), 0.264 (DCC)
R-Value Work: 0.219 (Depositor), 0.219 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.569	α = 90
b = 123.024	β = 91.05
c = 110.364	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Feng, Z.

Wilson, I.A.

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-004923
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI190286