7L2C

Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD)

PDB DOI: https://doi.org/10.2210/pdb7L2C/pdb

Classification: IMMUNE SYSTEM/Viral Protein
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-12-16 Released: 2021-02-10
Deposition Author(s): Cerutti, G., Reddem, E.R., Shapiro, L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.65 Å
R-Value Free: 0.272
R-Value Work: 0.216
R-Value Observed: 0.219

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: 177.33 kDa
Atom Count: 11,381
Modelled Residue Count: 1,428
Deposited Residue Count: 1,568
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, B	342	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
2-51 heavy chain	C [auth H], E [auth C]	227	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
2-51 light chain	D [auth L], F [auth D]	215	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: 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 [auth E]	2		N-Glycosylation	Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 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 AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] H [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain KB [auth C] MOL2 format, chain KB [auth C]	KB [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain KB [auth C] Interactions & Density Focus chain KB [auth C]
CAC (Subject of Investigation/LOI) Query on CAC Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A]	X [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain RB [auth D] SDF format, chain TA [auth H] SDF format, chain U [auth A] SDF format, chain UA [auth H] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain YA [auth L] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth H] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth L]	KA [auth B] LA [auth B] RB [auth D] TA [auth H] U [auth A] KA [auth B], LA [auth B], RB [auth D], TA [auth H], U [auth A], UA [auth H], V [auth A], W [auth A], YA [auth L]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain KA [auth B] Focus chain LA [auth B] Focus chain RB [auth D] Focus chain TA [auth H] Focus chain U [auth A] Focus chain UA [auth H] Focus chain V [auth A] Focus chain W [auth A] Focus chain YA [auth L] Interactions & Density Focus chain KA [auth B] Focus chain LA [auth B] Focus chain RB [auth D] Focus chain TA [auth H] Focus chain U [auth A] Focus chain UA [auth H] Focus chain V [auth A] Focus chain W [auth A] Focus chain YA [auth L]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain LB [auth D] SDF format, chain MA [auth H] SDF format, chain MB [auth D] SDF format, chain NA [auth H] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth H] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth H] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth H] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth H] SDF format, chain S [auth A] SDF format, chain SA [auth H] SDF format, chain T [auth A] SDF format, chain VA [auth L] SDF format, chain WA [auth L] SDF format, chain XA [auth L] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain LB [auth D] MOL2 format, chain MA [auth H] MOL2 format, chain MB [auth D] MOL2 format, chain NA [auth H] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth H] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth L] MOL2 format, chain WA [auth L] MOL2 format, chain XA [auth L] MOL2 format, chain ZA [auth C]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EA [auth B] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EA [auth B], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], LB [auth D], MA [auth H], MB [auth D], NA [auth H], NB [auth D], O [auth A], OA [auth H], OB [auth D], P [auth A], PA [auth H], PB [auth D], Q [auth A], QA [auth H], QB [auth D], R [auth A], RA [auth H], S [auth A], SA [auth H], T [auth A], VA [auth L], WA [auth L], XA [auth L], ZA [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain LB [auth D] Focus chain MA [auth H] Focus chain MB [auth D] Focus chain NA [auth H] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth H] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth H] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth H] Focus chain S [auth A] Focus chain SA [auth H] Focus chain T [auth A] Focus chain VA [auth L] Focus chain WA [auth L] Focus chain XA [auth L] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain LB [auth D] Focus chain MA [auth H] Focus chain MB [auth D] Focus chain NA [auth H] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth H] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth H] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth H] Focus chain S [auth A] Focus chain SA [auth H] Focus chain T [auth A] Focus chain VA [auth L] Focus chain WA [auth L] Focus chain XA [auth L] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.65 Å
R-Value Free: 0.272
R-Value Work: 0.216
R-Value Observed: 0.219
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.791	α = 90
b = 115.785	β = 99.97
c = 137.606	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-02-10

Deposition Author(s):

Cerutti, G.

Reddem, E.R.

Shapiro, L.

Funding Organization	Location	Grant Number
Other private	China	Jack Ma Foundation

Revision History (Full details and data files)

Version 1.0: 2021-02-10
Type: Initial release
Version 1.1: 2021-03-24
Changes: Database references
Version 1.2: 2021-04-14
Changes: Database references
Version 1.3: 2021-05-26
Changes: Database references
Version 1.4: 2023-10-18
Changes: Data collection, Database references, Refinement description