5W5W

HIV Protease (PR) in open form with Mg2+ in active site and HIVE-9 in eye site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 proteaseAB99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3TL
Query on 3TL

Download CCD File 
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
 Ligand Interaction
HV9
Query on HV9

Download CCD File 
A
4-methyl-N-({1-[4-(trifluoromethyl)pyrimidin-2-yl]piperidin-4-yl}carbamoyl)benzene-1-sulfonamide
C18 H20 F3 N5 O3 S
YEGSVKBKIFWARL-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.846α = 90
b = 65.542β = 90
c = 92.876γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SHELXPREPdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1P50GM103368

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Structure summary
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence