3L3V | pdb_00003l3v

Structure of HIV-1 integrase core domain in complex with sucrose

PDB DOI: https://doi.org/10.2210/pdb3L3V/pdb

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-12-18 Released: 2010-03-31
Deposition Author(s): Wielens, J., Chalmers, D.K., Scanlon, M.J., Parker, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.244 (Depositor), 0.244 (DCC)
R-Value Work:
0.194 (Depositor), 0.193 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site

Wielens, J., Headey, S.J., Jeevarajah, D., Rhodes, D.I., Deadman, J., Chalmers, D.K., Scanlon, M.J., Parker, M.W.

(2010) FEBS Lett 584: 1455-1462

PubMed: 20227411 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2010.03.016
Primary Citation Related Structures:
3L3U, 3L3V

PubMed Abstract:
HIV integrase (IN) is an essential enzyme in HIV replication and an important target for drug design. IN has been shown to interact with a number of cellular and viral proteins during the integration process. Disruption of these important interactions could provide a mechanism for allosteric inhibition of IN. We present the highest resolution crystal structure of the IN core domain to date. We also present a crystal structure of the IN core domain in complex with sucrose which is bound at the dimer interface in a region that has previously been reported to bind integrase inhibitors.

Organizational Affiliation

Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia.

Macromolecule Content

Total Structure Weight: 36.59 kDa
Atom Count: 2,331
Modeled Residue Count: 284
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POL polyprotein	A, B	163	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth B], I [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	C	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.244 (Depositor), 0.244 (DCC)
R-Value Work: 0.194 (Depositor), 0.193 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.085	α = 90
b = 60.714	β = 90
c = 81.463	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-02-12
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2021-11-10
Changes: Database references, Structure summary
Version 2.2: 2023-11-01
Changes: Data collection, Refinement description