5VCK | pdb_00005vck

HIV Protease (PR) with TL-3 in the active site and (Z)-N-(thiazol-2-yl)-N'-tosylcarbamimidate in the exosite

• PDB DOI: https://doi.org/10.2210/pdb5VCK/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-03-31 Released: 2018-04-18 
• Deposition Author(s): Tiefenbrunn, T., Stout, C.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Fragment-based campaign for the identification of potential exosite binders of HIV-1 Protease

Forli, S., Tiefenbrunn, T., Baksh, M.M., Chang, M.W., Perryman, A., Garg, D., Happer, M., Lin, Y.-C., Goodsell, D., Angelina, E.L., De Vera, I., Kojetin, D., Torbett, B.E., Finn, M.G., Elder, J., Stout, C.D., Olson, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 23.17 kDa 
• Atom Count: 1,666 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: pol EC: 3.4.23.16
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3TL	C [auth A]	benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate C50 H64 N6 O10 BJJPNOGMLLUCER-KUTQPOQPSA-N
7GC	D [auth A], E [auth B]	4-methyl-N-(thiazol-2-ylcarbamoyl)benzenesulfonamide C11 H11 N3 O3 S2 ZXPLKYLPCUVOFS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000434 (3TL)	C [auth A]	N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.953	α = 90
b = 62.953	β = 90
c = 82.306	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
autoXDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Tiefenbrunn, T., Stout, C.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1P50GM103368

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description