7YD3 | pdb_00007yd3

Single-chain variable fragment of app 3D1 antibody

PDB DOI: https://doi.org/10.2210/pdb7YD3/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-07-03 Released: 2023-07-05
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: 2.16 Å
R-Value Free:
0.254 (Depositor), 0.250 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A broadly neutralizing antibody recognizes a unique epitope with a signature motif common across coronaviruses

Yan, L., Wang, F., Hill, M., Brun, J., Liang, Z., Shi, X., Zhang, L., He, X., Li, Y., Huang, Q., Dong, X., Liu, H., Zhang, Y., Liu, L., Dwek, R.A., Zitzmann, N., Liang, A., Yang, G.

(2025) Nat Commun 16: 7580

DOI: https://doi.org/10.1038/s41467-025-63101-1

Macromolecule Content

Total Structure Weight: 98.96 kDa
Atom Count: 7,529
Modeled Residue Count: 915
Deposited Residue Count: 924
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of 3D1 scFv	A [auth H], C [auth A], E [auth C], G [auth E]	120	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of 3D1 scFv	B [auth L], D [auth B], F [auth D], H [auth F]	111	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 I [auth H] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain I [auth H] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain I [auth H] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	I [auth H], K [auth A], O [auth B], P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain I [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain U [auth F] SDF format, chain T [auth F] MOL2 format, chain J [auth H] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] mmCIF format, chain J [auth H] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F]	J [auth H] L [auth A] M [auth A] N [auth A] Q [auth B] J [auth H], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth C], T [auth F], U [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain J [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain T [auth F] Focus chain U [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]