8CWK

Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD)

PDB DOI: https://doi.org/10.2210/pdb8CWK/pdb

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

Deposited: 2022-05-19 Released: 2023-05-24
Deposition Author(s): Langley, D.B., Christ, D.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.223
R-Value Work: 0.186
R-Value Observed: 0.188

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Neutralization of CoV-2 omicron sublineages by affinity-matured class 5 antibodies

Langley, D.B., Christ, D.

To be published.

Macromolecule Content

Total Structure Weight: 120.46 kDa
Atom Count: 8,339
Modelled Residue Count: 1,066
Deposited Residue Count: 1,094
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab arm of antibody 10G4	A [auth H]	228	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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab arm of antibody 10G4	B [auth L]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth L]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab arm of antibody 4G1-C2	C [auth A]	232	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab arm of antibody 4G1-C2	D [auth B]	215	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6GMX0 (Homo sapiens) Explore Q6GMX0 Go to UniProtKB: Q6GMX0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6GMX0
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	E [auth C]	204	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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E [auth C]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain L [auth C] MOL2 format, chain G [auth L] MOL2 format, chain L [auth C] mmCIF format, chain G [auth L] mmCIF format, chain L [auth C]	G [auth L], L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth L] Focus chain L [auth C] Interactions & Density Focus chain G [auth L] Focus chain L [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] MOL2 format, chain F [auth H] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] mmCIF format, chain F [auth H] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C]	F [auth H] H [auth L] I [auth L] J [auth A] K [auth B] F [auth H], H [auth L], I [auth L], J [auth A], K [auth B], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Interactions & Density Focus chain F [auth H] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C]