8RJ7 | pdb_00008rj7

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29

PDB DOI: https://doi.org/10.2210/pdb8RJ7/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Camelus dromedarius
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-12-20 Released: 2024-11-27
Deposition Author(s): Casasnovas, J.M., Fernandez, L.A., Silva, K.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.222 (Depositor), 0.221 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Models: 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

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29

Casasnovas, J.M., Fernandez, L.A., Silva, K.

To be published.

Macromolecule Content

Total Structure Weight: 182.11 kDa
Atom Count: 13,135
Modeled Residue Count: 1,574
Deposited Residue Count: 1,645
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B [auth C], C [auth E], D [auth G], I	203	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C [auth E] Focus chain D [auth G] Focus chain I	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Camel-derived nanobody 1.29	E [auth B], F [auth D], G [auth F], H, J	126	Camelus dromedarius	Mutation(s): 0

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 K [auth A] SDF format, chain N [auth C] SDF format, chain O [auth E] SDF format, chain U [auth I] SDF format, chain Q [auth G] MOL2 format, chain K [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth E] MOL2 format, chain U [auth I] MOL2 format, chain Q [auth G] mmCIF format, chain K [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth E] mmCIF format, chain U [auth I] mmCIF format, chain Q [auth G]	K [auth A], N [auth C], O [auth E], Q [auth G], U [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain N [auth C] Focus chain O [auth E] Focus chain Q [auth G] Focus chain U [auth I] Interactions & Density Focus chain K [auth A] Focus chain N [auth C] Focus chain O [auth E] Focus chain Q [auth G] Focus chain U [auth I]
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain P [auth E] SDF format, chain R [auth B] SDF format, chain S [auth D] SDF format, chain T [auth H] MOL2 format, chain L [auth A] MOL2 format, chain P [auth E] MOL2 format, chain R [auth B] MOL2 format, chain S [auth D] MOL2 format, chain T [auth H] mmCIF format, chain L [auth A] mmCIF format, chain P [auth E] mmCIF format, chain R [auth B] mmCIF format, chain S [auth D] mmCIF format, chain T [auth H]	L [auth A], P [auth E], R [auth B], S [auth D], T [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain P [auth E] Focus chain R [auth B] Focus chain S [auth D] Focus chain T [auth H] Interactions & Density Focus chain L [auth A] Focus chain P [auth E] Focus chain R [auth B] Focus chain S [auth D] Focus chain T [auth H]