6YZ7

H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex

PDB DOI: https://doi.org/10.2210/pdb6YZ7/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens, Lama glama
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2020-05-06 Released: 2020-06-03
Deposition Author(s): Naismith, J.H., Ren, J., Zhou, D., Zhao, Y., Stuart, D.I.
Funding Organization(s): Wellcome Trust, Engineering and Physical Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.269
R-Value Work: 0.238

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2

Naismith, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 175.39 kDa
Atom Count: 11,718
Modelled Residue Count: 1,514
Deposited Residue Count: 1,586
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth AAA], E [auth EEE]	210	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 A [auth AAA] Focus chain E [auth EEE]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Cr3022	B [auth BBB], G [auth HHH]	229	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody light chain	C [auth CCC], H [auth LLL]	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	D [auth DDD], F [auth FFF]	134	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 I [auth AAA] SDF format, chain J [auth EEE] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth EEE] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth EEE]	I [auth AAA], J [auth EEE]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth AAA] Focus chain J [auth EEE] Interactions & Density Focus chain I [auth AAA] Focus chain J [auth EEE]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.269
R-Value Work: 0.238
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.598	α = 90
b = 154.598	β = 90
c = 229.312	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	100209/Z/12/Z
Engineering and Physical Sciences Research Council	United Kingdom	EP/S025243/1.

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary