5VEA

HIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,2-diamine in exosite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 protease
A
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 1 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
3TL
Query on 3TL

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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
TL-3, C2 symmetric inhibitor
C50 H64 N6 O10
BJJPNOGMLLUCER-KUTQPOQPSA-N
 Ligand Interaction
9AY
Query on 9AY

Download SDF File 
Download CCD File 
A
4-methylbenzene-1,2-diamine
C7 H10 N2
DGRGLKZMKWPMOH-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000434 (3TL)
Query on PRD_000434
AN-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.215 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 62.763α = 90.00
b = 62.763β = 90.00
c = 82.238γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
SCALAdata scaling
MOSFLMdata collection
MOLREPdata processing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-04-04 
  • Released Date: 2018-04-25 
  • Deposition Author(s): Stout, C.D.

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release