7BEK

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 2)

PDB DOI: https://doi.org/10.2210/pdb7BEK/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2020-12-23 Released: 2021-03-03
Deposition Author(s): Zhou, D., Zhao, Y., Ren, J., Stuart, D.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.220
R-Value Work: 0.200
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 71.65 kDa
Atom Count: 5,181
Modelled Residue Count: 628
Deposited Residue Count: 641
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-158 heavy chain	A [auth H]	222	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-158 light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth E]	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	3		N-Glycosylation	Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain P [auth E] MOL2 format, chain P [auth E]	P [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain P [auth E] Interactions & Density Focus chain P [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain K [auth L] SDF format, chain R [auth E] MOL2 format, chain E [auth H] MOL2 format, chain K [auth L] MOL2 format, chain R [auth E]	E [auth H], K [auth L], R [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain K [auth L] Focus chain R [auth E] Interactions & Density Focus chain E [auth H] Focus chain K [auth L] Focus chain R [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain M [auth L] MOL2 format, chain G [auth H] MOL2 format, chain M [auth L]	G [auth H], M [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth H] Focus chain M [auth L] Interactions & Density Focus chain G [auth H] Focus chain M [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain L SDF format, chain Q [auth E] MOL2 format, chain F [auth H] MOL2 format, chain L MOL2 format, chain Q [auth E]	F [auth H], L, Q [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Focus chain L Focus chain Q [auth E] Interactions & Density Focus chain F [auth H] Focus chain L Focus chain Q [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain S [auth E] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain S [auth E]	H I [auth H] J [auth H] N [auth L] O [auth L] H, I [auth H], J [auth H], N [auth L], O [auth L], S [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain N [auth L] Focus chain O [auth L] Focus chain S [auth E] Interactions & Density Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain N [auth L] Focus chain O [auth L] Focus chain S [auth E]