6VW1

Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2

PDB DOI: https://doi.org/10.2210/pdb6VW1/pdb

Classification: CELL INVASION
Organism(s): Homo sapiens, Severe acute respiratory syndrome-related coronavirus, Severe acute respiratory syndrome coronavirus 2
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2020-02-18 Released: 2020-03-04
Deposition Author(s): Shang, J., Ye, G., Shi, K., Wan, Y.S., Aihara, H., Li, F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.229
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Currently 6VW1 does not have a validation slider image.

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 192.75 kDa
Atom Count: 13,180
Modelled Residue Count: 1,579
Deposited Residue Count: 1,628
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A, B	597	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 chimeric RBD	C [auth E], D [auth F]	217	Severe acute respiratory syndrome-related coronavirus, Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2 Membrane Entity: Yes
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594 Go to UniProtKB: P59594
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 Groups	P0DTC2P59594
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], F [auth D], L	3		N-Glycosylation	Interactions Focus chain E [auth C] Focus chain F [auth D] Focus chain L Interactions & Density Focus chain E [auth C] Focus chain F [auth D] Focus chain L
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, K, M	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain K Focus chain M Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain K Focus chain M
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	4		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G25906YW GlyCosmos: G25906YW

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	Q [auth A], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B]	N [auth A], R [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain R [auth B] Interactions & Density Focus chain N [auth A] Focus chain R [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B]	P [auth A], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain S [auth B] MOL2 format, chain O [auth A] MOL2 format, chain S [auth B]	O [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth A] Focus chain S [auth B] Interactions & Density Focus chain O [auth A] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.229
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.435	α = 90
b = 118.034	β = 93.12
c = 112.075	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
REFMAC	refinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01AI089728
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01AI089728
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047

Revision History (Full details and data files)

Version 1.0: 2020-03-04
Type: Initial release
Version 1.1: 2020-03-11
Changes: Source and taxonomy
Version 1.2: 2020-04-08
Changes: Database references, Structure summary
Version 1.3: 2020-04-15
Changes: Database references, Structure summary
Version 1.4: 2020-05-06
Changes: Database references, Source and taxonomy, Structure summary
Version 1.5: 2020-05-27
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary