3WNH

Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase

PDB DOI: https://doi.org/10.2210/pdb3WNH/pdb

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

Deposited: 2013-12-10 Released: 2013-12-25
Deposition Author(s): Wielens, J., Chalmers, D.K., Parker, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.227
R-Value Work: 0.190
R-Value Observed: 0.192

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 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.

Macromolecule Content

Total Structure Weight: 36.67 kDa
Atom Count: 2,480
Modelled Residue Count: 283
Deposited Residue Count: 326
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PK(NLE)DN(DVA) peptide	C, D	6	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth A], F [auth A], K [auth B], L [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	H [auth A] I [auth A] J [auth A] N [auth B] O [auth B] 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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE Query on NLE	C, D	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001213 Query on PRD_001213	C, D	PK(NLE)DN(DVA) peptide	Cyclic peptide / Inhibitor		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.227
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.44	α = 90
b = 49.44	β = 90
c = 101.33	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Wielens, J.

Chalmers, D.K.

Parker, M.W.

Revision History (Full details and data files)

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: 2023-12-06
Changes: Data collection

Prepare Data

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Deposit Data

Help and Resources

3WNH

Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase

Hexapeptide mimetics of LEDGF in complex with HIV-1 integrase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2