8F2V | pdb_00008f2v

Antibody Fab directed against SARS-CoV-2 Spike Protein Receptor Binding Domain (RBD)

PDB DOI: https://doi.org/10.2210/pdb8F2V/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-11-08 Released: 2023-12-13
Deposition Author(s): Chen, J.C.-H.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.289 (Depositor), 0.290 (DCC)
R-Value Work:
0.246 (Depositor), 0.250 (DCC)
R-Value Observed:
0.249 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Antibody Fab directed against SARS-CoV-2 Spike Protein Receptor Binding Domain (RBD)

Chen, J.C.-H.

To be published.

Macromolecule Content

Total Structure Weight: 139.96 kDa
Atom Count: 9,720
Modeled Residue Count: 1,296
Deposited Residue Count: 1,311
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	A [auth C], C [auth A], E	214	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	B [auth D], D [auth B], F	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth A] SDF format, chain I [auth F] MOL2 format, chain G [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth F] mmCIF format, chain G [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth F]	G [auth C], H [auth A], I [auth F]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth A] Focus chain I [auth F] Interactions & Density Focus chain G [auth C] Focus chain H [auth A] Focus chain I [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.289 (Depositor), 0.290 (DCC)
R-Value Work: 0.246 (Depositor), 0.250 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.011	α = 90
b = 184.182	β = 90
c = 181.064	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

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.