7VZT | pdb_00007vzt

A human neutralizing antibody targeting SARS-CoV-2 RBD

PDB DOI: https://doi.org/10.2210/pdb7VZT/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Eukaryota sp.
Mutation(s): No

Deposited: 2021-11-16 Released: 2023-05-31
Deposition Author(s): Wang, F.Z., Wang, Y., Tan, X.W., Shi, R., Yan, J.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.41 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.217 (Depositor), 0.218 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7VZT

This is version 1.2 of the entry. See complete history.

Literature

GH12, glycosylation function

Wang, F.Z., Tan, X.W., Shi, R.

To be published.

Macromolecule Content

Total Structure Weight: 68.64 kDa
Atom Count: 4,768
Modeled Residue Count: 627
Deposited Residue Count: 627
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	200	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GH12-Heavy	B	212	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GH12-LIGHT	C	215	Homo sapiens	Mutation(s): 0

Oligosaccharides

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.41 Å
R-Value Free: 0.263 (Depositor), 0.263 (DCC)
R-Value Work: 0.217 (Depositor), 0.218 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.605	α = 90
b = 150.605	β = 90
c = 121.32	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-05-31
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.