6YLA

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab

PDB DOI: https://doi.org/10.2210/pdb6YLA/pdb

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

Deposited: 2020-04-06 Released: 2020-04-15
Deposition Author(s): Huo, J., Zhao, Y., Ren, J., Zhou, D., Ginn, H.M., Fry, E.E., Owens, R., Stuart, D.I.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.237
R-Value Work: 0.213
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 149.08 kDa
Atom Count: 10,090
Modelled Residue Count: 1,273
Deposited Residue Count: 1,324
Unique protein chains: 3

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], D [auth A]	213	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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain	B [auth H], E [auth B]	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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(by identity cutoff) | 3D Structure

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain V [auth L] MOL2 format, chain GA [auth C] MOL2 format, chain V [auth L]	GA [auth C], V [auth L]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain V [auth L] Interactions & Density Focus chain GA [auth C] Focus chain V [auth L]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain M [auth E] SDF format, chain Z [auth A] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain Z [auth A]	L [auth E], M [auth E], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth E] Focus chain M [auth E] Focus chain Z [auth A] Interactions & Density Focus chain L [auth E] Focus chain M [auth E] Focus chain Z [auth A]
PG0 Query on PG0 Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A]	X [auth A]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain I [auth E] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain N [auth E] SDF format, chain O [auth H] SDF format, chain R [auth H] SDF format, chain S [auth H] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain I [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth E] MOL2 format, chain O [auth H] MOL2 format, chain R [auth H] MOL2 format, chain S [auth H]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] I [auth E] BA [auth B], CA [auth B], DA [auth B], EA [auth B], I [auth E], JA [auth C], KA [auth C], LA [auth C], N [auth E], O [auth H], R [auth H], S [auth H]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain I [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth E] Focus chain O [auth H] Focus chain R [auth H] Focus chain S [auth H] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain I [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth E] Focus chain O [auth H] Focus chain R [auth H] Focus chain S [auth H]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth E] SDF format, chain H [auth E] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain J [auth E] SDF format, chain K [auth E] SDF format, chain P [auth H] SDF format, chain Q [auth H] SDF format, chain T [auth L] SDF format, chain U [auth L] SDF format, chain W [auth A] SDF format, chain Y [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth E] MOL2 format, chain H [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth E] MOL2 format, chain K [auth E] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain T [auth L] MOL2 format, chain U [auth L] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A]	AA [auth A] FA [auth B] G [auth E] H [auth E] HA [auth C] AA [auth A], FA [auth B], G [auth E], H [auth E], HA [auth C], IA [auth C], J [auth E], K [auth E], P [auth H], Q [auth H], T [auth L], U [auth L], W [auth A], Y [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain FA [auth B] Focus chain G [auth E] Focus chain H [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth E] Focus chain K [auth E] Focus chain P [auth H] Focus chain Q [auth H] Focus chain T [auth L] Focus chain U [auth L] Focus chain W [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth A] Focus chain FA [auth B] Focus chain G [auth E] Focus chain H [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth E] Focus chain K [auth E] Focus chain P [auth H] Focus chain Q [auth H] Focus chain T [auth L] Focus chain U [auth L] Focus chain W [auth A] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.237
R-Value Work: 0.213
R-Value Observed: 0.214
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.124	α = 90
b = 163.124	β = 90
c = 189.076	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1

Revision History (Full details and data files)

Version 1.0: 2020-04-15
Type: Initial release
Version 1.1: 2020-05-06
Changes: Database references, Source and taxonomy, Structure summary
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2020-10-28
Changes: Database references, Structure summary
Version 1.4: 2024-01-24
Changes: Data collection, Database references, Refinement description