3WNE | pdb_00003wne

Cyclic hexapeptide PKIDNG in complex with HIV-1 integrase

• PDB DOI: https://doi.org/10.2210/pdb3WNE/pdb

• Classification: Viral Protein/Peptide
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-12-09 Released: 2013-12-25 
• Deposition Author(s): Wielens, J., Chalmers, D.K., Parker, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.228 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.59 kDa 
• Atom Count: 2,370 
• Modeled Residue Count: 282 
• Deposited Residue Count: 326 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag-Pol polyprotein	A, B	157	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 7  Gene Names: HIV-1 POL
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LEDGF peptide	C, D	6	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	E [auth A], F [auth A], K [auth B], L [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001211	C, D	LEDGF peptide	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.228 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.68	α = 90
b = 49.68	β = 90
c = 102.93	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Wielens, J., Chalmers, D.K., Parker, M.W.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary