8Z9L | pdb_00008z9l

Crystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2

PDB DOI: https://doi.org/10.2210/pdb8Z9L/pdb

Classification: VIRAL PROTEIN/HYDROLASE
Organism(s): Rhinolophus affinis, Severe acute respiratory syndrome coronavirus 2
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-04-23 Released: 2025-04-30
Deposition Author(s): Lan, J., Wang, C.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.277 (Depositor), 0.278 (DCC)
R-Value Work:
0.242 (Depositor), 0.244 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2

Lan, J., Wang, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 369.81 kDa
Atom Count: 25,939
Modelled Residue Count: 3,168
Deposited Residue Count: 3,180
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	A [auth B], C [auth I], E [auth O], G [auth U]	598	Rhinolophus affinis	Mutation(s): 0 EC: 3.4
UniProt
Find proteins for A0A7D7JS29 (Rhinolophus affinis) Explore A0A7D7JS29 Go to UniProtKB: A0A7D7JS29
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7D7JS29
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth B] Focus chain E [auth O] Focus chain G [auth U]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth F], D [auth L], F [auth R], H [auth X]	197	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth L] Focus chain F [auth R]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth A], J [auth C]	2		N-Glycosylation	Interactions Focus chain I [auth A] Focus chain J [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth C]

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth I] SDF format, chain N [auth I] SDF format, chain O [auth L] SDF format, chain P [auth O] SDF format, chain Q [auth O] SDF format, chain R [auth O] SDF format, chain S [auth R] SDF format, chain T [auth U] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth I] MOL2 format, chain N [auth I] MOL2 format, chain O [auth L] MOL2 format, chain P [auth O] MOL2 format, chain Q [auth O] MOL2 format, chain R [auth O] MOL2 format, chain S [auth R] MOL2 format, chain T [auth U] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth I] mmCIF format, chain N [auth I] mmCIF format, chain O [auth L] mmCIF format, chain P [auth O] mmCIF format, chain Q [auth O] mmCIF format, chain R [auth O] mmCIF format, chain S [auth R] mmCIF format, chain T [auth U]	K [auth B] L [auth B] M [auth I] N [auth I] O [auth L] K [auth B], L [auth B], M [auth I], N [auth I], O [auth L], P [auth O], Q [auth O], R [auth O], S [auth R], T [auth U]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth I] Focus chain N [auth I] Focus chain O [auth L] Focus chain P [auth O] Focus chain Q [auth O] Focus chain R [auth O] Focus chain S [auth R] Focus chain T [auth U] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth I] Focus chain N [auth I] Focus chain O [auth L] Focus chain P [auth O] Focus chain Q [auth O] Focus chain R [auth O] Focus chain S [auth R] Focus chain T [auth U]