2QMP

Crystal Structure of HIV-1 protease complexed with PL-100

PDB DOI: https://doi.org/10.2210/pdb2QMP/pdb

Classification: HYDROLASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-07-16 Released: 2008-07-22
Deposition Author(s): Allison, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.248
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of HIV-1 protease complexed with PL-100

Coburn, C.A., Allison, T.J., Holloway, M.K., Wu, J.J., Wainberg, M.A., Vacca, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 22.91 kDa
Atom Count: 1,850
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pol polyprotein	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0 EC: 3.4.23.16
UniProt
Find proteins for Q9WFL7 (Human immunodeficiency virus 1) Explore Q9WFL7 Go to UniProtKB: Q9WFL7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WFL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A00 Query on A00 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	N-[(5S)-5-{[(4-aminophenyl)sulfonyl](isobutyl)amino}-6-hydroxyhexyl]-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide C₃₃ H₄₄ N₄ O₆ S QAHLFXYLXBBCPS-IZEXYCQBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
A00	BindingDB: 2QMP	IC50: 0.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.248
R-Value Work: 0.205
R-Value Observed: 0.207
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.79	α = 90
b = 85.98	β = 90
c = 46.19	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-22

Deposition Author(s):

Allison, T.J.

Revision History (Full details and data files)

Version 1.0: 2008-07-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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2QMP

Crystal Structure of HIV-1 protease complexed with PL-100

Crystal Structure of HIV-1 protease complexed with PL-100

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)