7YI6

bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein

PDB DOI: https://doi.org/10.2210/pdb7YI6/pdb

Classification: ANTIVIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human coronavirus 229E, Homo sapiens
Expression System: chemical production metagenome, Homo sapiens
Mutation(s): No

Deposited: 2022-07-15 Released: 2023-08-30
Deposition Author(s): Yan, L., Yang, G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.220
R-Value Work: 0.193
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cross-reactive epitopes between HIV and Coronavirus revealed by 3D1

Yan, L., Yang, G.

To be published.

Macromolecule Content

Total Structure Weight: 93.66 kDa
Atom Count: 6,923
Modelled Residue Count: 869
Deposited Residue Count: 884
Unique protein chains: 3

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, D [auth C]	7	Human coronavirus 229E	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P15423 (Human coronavirus 229E) Explore P15423 Go to UniProtKB: P15423
Entity Groups
UniProt Group	P15423
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of 3D1	B, E	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of 3D1	C [auth D], F	221	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth E] MOL2 format, chain L [auth E] mmCIF format, chain L [auth E]	L [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth E] Interactions & Density Focus chain L [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain M [auth E] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain M [auth E] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain M [auth E]	G [auth B], H [auth B], J [auth D], K [auth D], M [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth E] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]