6VLH

HIV Integrase Core domain (IN) in complex with dimer-spanning ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor

Scanlon, M.Gorman, M.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseA, B164Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
EC: 2.7.7.49
UniProt
Find proteins for F2WR39 (Human immunodeficiency virus 1)
Explore F2WR39 
Go to UniProtKB:  F2WR39
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R2A
Query on R2A

Download Ideal Coordinates CCD File 
R [auth B](2-{[3-(4-{2-[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzene-1-carbonyl)amino]ethyl}piperazine-1-carbonyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid
C46 H39 N3 O8
FKZRCFVPEMPOMA-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], K [auth B], L [auth B]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , M [auth B] , N [auth B] , O [auth B] , P [auth B] , 
G [auth A],  H [auth A],  I [auth A],  J [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.223 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.306α = 90
b = 46.306β = 90
c = 139.148γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release