8BUV | pdb_00008buv

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3

PDB DOI: https://doi.org/10.2210/pdb8BUV/pdb

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-11-30 Released: 2023-12-13
Deposition Author(s): Singer, M.R., Pye, V.E., Cook, N.J., Cherepanov, P.
Funding Organization(s): Cancer Research UK, Medical Research Council (MRC, United Kingdom), Wellcome Trust, The Francis Crick Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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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 Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3

Singer, M.R., Cherepanov, P.

To be published.

Macromolecule Content

Total Structure Weight: 104.67 kDa
Atom Count: 3,406
Modeled Residue Count: 398
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B, C, D	233	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: gag-pol EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
723 (Subject of Investigation/LOI) Query on 723 Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B]	J [auth B], N [auth D]	(6-chloro-2-oxo-4-phenyl-1,2-dihydroquinolin-3-yl)acetic acid C₁₇ H₁₂ Cl N O₃ SHDUUQWYFNJIAG-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth D] Interactions & Density Focus chain J [auth B] Focus chain N [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B] G [auth B] H [auth B] I [auth B] K [auth C] F [auth B], G [auth B], H [auth B], I [auth B], K [auth C], M [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain E [auth B] MOL2 format, chain L [auth D] MOL2 format, chain E [auth B] mmCIF format, chain L [auth D] mmCIF format, chain E [auth B]	E [auth B], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain L [auth D] Interactions & Density Focus chain E [auth B] Focus chain L [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
723	BindingDB: 8BUV	IC50: 1.17e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.247 (Depositor), 0.250 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.84	α = 90
b = 65.16	β = 99.9
c = 69.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	FC001061
Medical Research Council (MRC, United Kingdom)	United Kingdom	FC001061
Wellcome Trust	United Kingdom	FC001061
The Francis Crick Institute	United Kingdom	FC001061