8S9Q

HIV-1 Integrase Catalytic Core Domain (CCD) F185H Mutant Complexed with STP03-0404

PDB DOI: https://doi.org/10.2210/pdb8S9Q/pdb

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

Deposited: 2023-03-29 Released: 2024-02-07
Deposition Author(s): Dinh, T., 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: 2.26 Å
R-Value Free: 0.293
R-Value Work: 0.255
R-Value Observed: 0.259

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

HIV-1 Integrase Catalytic Core Domain Complexed with STP-0404

Dinh, T., Kvaratskhelia, M.

To be published.

Macromolecule Content

Total Structure Weight: 18.42 kDa
Atom Count: 1,130
Modelled Residue Count: 132
Deposited Residue Count: 163
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	163	Human immunodeficiency virus 1	Mutation(s): 1
UniProt
Find proteins for Q76353 (Human immunodeficiency virus 1) Explore Q76353 Go to UniProtKB: Q76353
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q76353
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WBV (Subject of Investigation/LOI) Query on WBV Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(2S)-tert-butoxy{4-(4-chlorophenyl)-2,3,6-trimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid C₂₇ H₃₁ Cl N₄ O₃ GNRDGAWRAIJOSU-DEOSSOPVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.293
R-Value Work: 0.255
R-Value Observed: 0.259
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.991	α = 90
b = 71.991	β = 90
c = 65.92	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Kvaratskhelia, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI143649

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release
Version 1.1: 2024-02-14
Changes: Database references

RCSB PDB Core Operations are 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.