2QMP | pdb_00002qmp

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 (Depositor), 0.246 (DCC)
R-Value Work:
0.205 (Depositor), 0.203 (DCC)
R-Value Observed:
0.207 (Depositor)

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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
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 type 1) Explore Q9WFL7 Go to UniProtKB: Q9WFL7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.248 (Depositor), 0.246 (DCC)
R-Value Work: 0.205 (Depositor), 0.203 (DCC)
R-Value Observed: 0.207 (Depositor)

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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Entry History

Deposition Data

Released Date: 2008-07-22

Deposition Author(s):

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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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.