3WNE

Cyclic hexapeptide PKIDNG in complex with HIV-1 integrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Hexapeptide mimetics of LEDGF in complex with HIV-1 integrase

Northfield, S.E.Wielens, J.Headey, S.J.Mulcair, M.Scanlon, M.J.Parker, M.W.Thompson, P.E.Chalmers, D.K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag-Pol polyprotein
A, B
157Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 7 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LEDGF peptide
C, D
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001211
Query on PRD_001211
C,DLEDGF peptideCyclic peptide / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 49.680α = 90.00
b = 49.680β = 90.00
c = 102.930γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
AMoREphasing
REFMACrefinement
Blu-Icedata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description