7LDJ

SARS-CoV-2 receptor binding domain in complex with WNb-2

PDB DOI: https://doi.org/10.2210/pdb7LDJ/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-01-13 Released: 2021-05-05
Deposition Author(s): Pymm, P., Dietrich, M.H., Tan, L.L., Adair, A., Tham, W.H.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.268
R-Value Work: 0.210
R-Value Observed: 0.213

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SARS-CoV-2 receptor binding domain in complex with WNb-2

Pymm, P., Adair, A., Chan, L.J., Cooney, J.P., Mordant, F.L., Allison, C.C., Lopez, E., Haycroft, E., O'Neill, M.T., Tan, L.L., Dietrich, M.H., Drew, D., Doerflinger, M., Dengler, M., Scott, N.E., Wheatley, A.K., Gherardin, N.A., Venugopal, H., Cromer, D., Davenport, M.P., Pickering, R., Godfrey, D.I., Purcell, D.J., Kent, S.J., Chung, A.W., Subbarao, K., Pellegrini, M., Glukhova, A., Tham, W.H.

(2021) Proc Natl Acad Sci U S A

DOI: https://doi.org/10.1073/pnas.210191811

Macromolecule Content

Total Structure Weight: 149.12 kDa
Atom Count: 10,429
Modelled Residue Count: 1,287
Deposited Residue Count: 1,320
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth A], C, D	199	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 B] Focus chain B [auth A] Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 2	E, F, G, H	131	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, K	4		N-Glycosylation	Interactions Focus chain I Focus chain K Interactions & Density Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G86566TX GlyCosmos: G86566TX GlyGen: G86566TX

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	6		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G80946QO GlyCosmos: G80946QO GlyGen: G80946QO

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 M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain N [auth E] MOL2 format, chain N [auth E] mmCIF format, chain N [auth E]	N [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain N [auth E] Interactions & Density Focus chain N [auth E]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.268
R-Value Work: 0.210
R-Value Observed: 0.213
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.12	α = 90
b = 88.508	β = 90.4
c = 107.488	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-05-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT2002073

Revision History (Full details and data files)

Version 1.0: 2021-05-05
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary