4Y1D | pdb_00004y1d

Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase core domain

• PDB DOI: https://doi.org/10.2210/pdb4Y1D/pdb

• Classification: TRANSFERASE/TRANSFERASE BINDING PROTEIN
• Organism(s): Human immunodeficiency virus 1, synthetic construct
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2015-02-07 Released: 2015-05-13 
• Deposition Author(s): Wielens, J., Chalmers, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.189 (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: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 38.06 kDa 
• Atom Count: 2,367 
• Modeled Residue Count: 289 
• Deposited Residue Count: 340 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B	167	Human immunodeficiency virus 1	Mutation(s): 4  Gene Names: 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
Cyclic hexapeptide cyc[NdPopPKID]	C [auth D]	6	synthetic construct	Mutation(s): 0

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
45W	C [auth D]	D-PEPTIDE LINKING	C7 H9 N O3		--
DVA	C [auth D]	D-PEPTIDE LINKING	C5 H11 N O2		--
NLE	C [auth D]	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.8	α = 90
b = 62.6	β = 90
c = 82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Wielens, J., Chalmers, D.K.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection, Derived calculations