Macromolecule Content

Total Structure Weight: 18.89 kDa
Atom Count: 1116
Modelled Residue Count: 131
Deposited Residue Count: 166
Unique protein chains: 1

6NUJ

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor BI-224436

PDB DOI: 10.2210/pdb6NUJ/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2019-02-01 Released: 2019-12-11
Deposition Author(s): Lindenberger, J.J., Kvaratskhelia, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.244
R-Value Work: 0.219
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors.

Koneru, P.C., Francis, A.C., Deng, N., Rebensburg, S.V., Hoyte, A.C., Lindenberger, J., Adu-Ampratwum, D., Larue, R.C., Wempe, M.F., Engelman, A.N., Lyumkis, D., Fuchs, J.R., Levy, R.M., Melikyan, G.B., Kvaratskhelia, M.

(2019) Elife 8

PubMed: 31120420 Search on PubMedSearch on PubMed Central
DOI: 10.7554/eLife.46344
Primary Citation of Related Structures:
6NUJ

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	166	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: pol
UniProt
Find proteins for F2WR52 (Human immunodeficiency virus 1) Explore F2WR52 Go to UniProtKB: F2WR52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F2WR52
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L3D Query on L3D Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(2S)-tert-butoxy[4-(2,3-dihydropyrano[4,3,2-de]quinolin-7-yl)-2-methylquinolin-3-yl]acetic acid C₂₇ H₂₆ N₂ O₄ MIXIIJCBELCMCZ-VWLOTQADSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF Query on CAF	A	L-PEPTIDE LINKING	C₅ H₁₂ As N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.244
R-Value Work: 0.219
R-Value Observed: 0.222
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.211	α = 90
b = 72.211	β = 90
c = 66.079	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
SCALEPACK	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Deposited Date: 2019-02-01
Released Date: 2019-12-11

Deposition Author(s):

Lindenberger, J.J.

Kvaratskhelia, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI110310

Revision History (Full details and data files)

Version 1.0: 2019-12-11
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.