5YB2: Crystal Structure Of LP-11/N44 - RCSB PDB

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227,561 Structures from the PDB 1,068,577 Computed Structure Models (CSM)

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Data API 5YB2

Crystal structure of LP-11/N44

• PDB DOI: https://doi.org/10.2210/pdb5YB2/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Mutation(s): No 
• Deposited: 2017-09-03 Released: 2018-02-28 
• Deposition Author(s): Zhang, X., Wang, X., He, Y.

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.307 
• R-Value Work: 0.283 
• R-Value Observed: 0.284 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history. LiteratureDownload Primary Citation 

•  Download Mendeley

Structural Insights into the Mechanisms of Action of Short-Peptide HIV-1 Fusion Inhibitors Targeting the Gp41 Pocket

Zhang, X., Zhu, Y., Hu, H., Zhang, S., Wang, P., Chong, H., He, J., Wang, X., He, Y.

(2018) Front Cell Infect Microbiol 8: 51-51

• PubMed: 29535974 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.3389/fcimb.2018.00051
• Primary Citation of Related Structures:  5YB2, 5YB3, 5YB4
• PubMed Abstract: 

  The deep hydrophobic pocket of HIV-1 gp41 has been considered a drug target, but short-peptides targeting this site usually lack potent antiviral activity. By applying the M-T hook structure, we previously generated highly potent short-peptide fusion inhibitors that specifically targeted the pocket site, such as MT-SC22EK, HP23L, and LP-11. Here, the crystal structures of HP23L and LP-11 bound to the target mimic peptide N36 demonstrated the critical intrahelical and interhelical interactions, especially verifying that the hook-like conformation was finely adopted while the methionine residue was replaced by the oxidation-less prone residue leucine, and that addition of an extra glutamic acid significantly enhanced the binding and inhibitory activities. The structure of HP23L bound to N36 with two mutations (E49K and L57R) revealed the critical residues and motifs mediating drug resistance and provided new insights into the mechanism of action of inhibitors. Therefore, the present data help our understanding for the structure-activity relationship (SAR) of HIV-1 fusion inhibitors and facilitate the development of novel antiviral drugs.

   View More
Organizational Affiliation: 

College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China.

Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report

Global Symmetry: Cyclic - C3 (Explore in 3D)Global Stoichiometry: Hetero 6-mer - A3B3 LessFind Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report

Global Symmetry: Cyclic - C3 (Explore in 3D)Global Stoichiometry: Hetero 6-mer - A3B3 LessFind Similar Assemblies

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report

Global Symmetry: Cyclic - C3 (Explore in 3D)Global Stoichiometry: Hetero 6-mer - A3B3 LessFind Similar Assemblies

Biological assembly 3 assigned by authors and generated by PISA (software)

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Macromolecule Content

• Total Structure Weight: 71.18 kDa 
• Atom Count: 3,495 
• Modelled Residue Count: 411 
• Deposited Residue Count: 584 
• Unique protein chains: 3

MacromoleculesFind similar proteins by: Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	A [auth E],B [auth D],G [auth B],H [auth A],M	67	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))Explore P04578 Go to UniProtKB:  P04578
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04578
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	C [auth F],I [auth C]	44	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))Explore P04578 Go to UniProtKB:  P04578
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04578
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LP-11	D [auth H]E [auth G]F [auth I]J [auth K]K [auth J]D [auth H],E [auth G],F [auth I],J [auth K],K [auth J],L,N [auth P] Less	23	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.307 
• R-Value Work: 0.283 
• R-Value Observed: 0.284 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.884	α = 90
b = 110.884	β = 90
c = 125.382	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental dataEntry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Zhang, X., Wang, X., He, Y.

Revision History (Full details and data files)

• Version 1.0: 2018-02-28Type: Initial release
• Version 1.1: 2018-03-28Changes: Database references
• Version 1.2: 2024-03-27Changes: Data collection, Database references

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