3WNG

Cyclic hexapeptide PKIDNp in complex with HIV-1 integrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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 (NEW YORK-5 ISOLATE)Mutation(s): 7 
Gene Names: HIV-1 POLgag-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 P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PKIDN(DPR) 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
CD
Query on CD

Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001214
Query on PRD_001214
C, DPKIDN(DPR) peptideCyclic peptide /  Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.25α = 90
b = 50.25β = 90
c = 102.71γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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