7BEP

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs

PDB DOI: https://doi.org/10.2210/pdb7BEP/pdb

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

Deposited: 2020-12-24 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: 2.61 Å
R-Value Free: 0.241
R-Value Work: 0.203
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 248.15 kDa
Atom Count: 16,957
Modelled Residue Count: 2,175
Deposited Residue Count: 2,242
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth E], F [auth C]	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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-384 heavy chain	B [auth A], G [auth D]	243	Homo sapiens	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-384 light chain	C [auth B], H [auth F]	227	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 heavy chain	D [auth H], I [auth G]	232	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 light chain	E [auth L], J [auth I]	214	Homo sapiens	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: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J], L [auth K]	6		N-Glycosylation	Interactions Focus chain K [auth J] Focus chain L [auth K] Interactions & Density Focus chain K [auth J] Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain PA [auth I] SDF format, chain Z [auth L] MOL2 format, chain PA [auth I] MOL2 format, chain Z [auth L]	PA [auth I], Z [auth L]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain PA [auth I] Focus chain Z [auth L] Interactions & Density Focus chain PA [auth I] Focus chain Z [auth L]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B]	R [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain P [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain P [auth A]	GA [auth D], P [auth A]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain GA [auth D] Focus chain P [auth A] Interactions & Density Focus chain GA [auth D] Focus chain P [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain FA [auth D] MOL2 format, chain FA [auth D]	FA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Interactions & Density Focus chain FA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain U [auth H] MOL2 format, chain IA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain U [auth H]	IA [auth F], KA [auth G], LA [auth G], U [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain U [auth H] Interactions & Density Focus chain IA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain U [auth H]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain JA [auth F] SDF format, chain MA [auth G] SDF format, chain OA [auth G] SDF format, chain Q [auth A] SDF format, chain W [auth H] MOL2 format, chain AA [auth L] MOL2 format, chain JA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth H]	AA [auth L] JA [auth F] MA [auth G] OA [auth G] Q [auth A] AA [auth L], JA [auth F], MA [auth G], OA [auth G], Q [auth A], W [auth H]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain JA [auth F] Focus chain MA [auth G] Focus chain OA [auth G] Focus chain Q [auth A] Focus chain W [auth H] Interactions & Density Focus chain AA [auth L] Focus chain JA [auth F] Focus chain MA [auth G] Focus chain OA [auth G] Focus chain Q [auth A] Focus chain W [auth H]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain M [auth E] SDF format, chain NA [auth G] SDF format, chain V [auth H] SDF format, chain X [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain M [auth E] MOL2 format, chain NA [auth G] MOL2 format, chain V [auth H] MOL2 format, chain X [auth H]	BA [auth C], M [auth E], NA [auth G], V [auth H], X [auth H]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain BA [auth C] Focus chain M [auth E] Focus chain NA [auth G] Focus chain V [auth H] Focus chain X [auth H] Interactions & Density Focus chain BA [auth C] Focus chain M [auth E] Focus chain NA [auth G] Focus chain V [auth H] Focus chain X [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain HA [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain QA [auth I] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth I] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth H]	CA [auth C] DA [auth D] EA [auth D] HA [auth F] N [auth A] CA [auth C], DA [auth D], EA [auth D], HA [auth F], N [auth A], O [auth A], QA [auth I], S [auth B], T [auth B], Y [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain QA [auth I] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth H] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain QA [auth I] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.241
R-Value Work: 0.203
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.76	α = 90
b = 113.221	β = 90
c = 302.773	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1
CAMS Innovation Fund for Medical Sciences (CIFMS)	China	2018-I2M-2-002

Revision History (Full details and data files)

Version 1.0: 2021-03-03
Type: Initial release
Version 1.1: 2021-04-07
Changes: Database references
Version 1.2: 2021-04-28
Changes: Database references
Version 1.3: 2024-01-31
Changes: Data collection, Database references, Refinement description