5W5W | pdb_00005w5w

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 (Depositor), 0.324 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5W5W

Ligand Structure Quality Assessment 


This is version 1.3 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.

Macromolecule Content 

  • Total Structure Weight: 22.97 kDa 
  • Atom Count: 1,617 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 protease
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3TL

Query on 3TL


Download:Ideal Coordinates CCD File
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
HV9

Query on HV9


Download:Ideal Coordinates CCD File
D [auth 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
DMS

Query on DMS


Download:Ideal Coordinates CCD File
E [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N

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 (Depositor), 0.324 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
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



Ligand Structure Quality Assessment 


View more in-depth experimental data

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  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description