7YD3

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
R-Value Work: 0.217
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

This is version 1.1 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: 98.96 kDa
Atom Count: 7,529
Modelled 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]	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 T [auth F] SDF format, chain U [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 T [auth F] MOL2 format, chain U [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]	S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]