3I2L

Crystal structure of a chemically synthesized [allo-Ile50/50']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor

PDB DOI: https://doi.org/10.2210/pdb3I2L/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human immunodeficiency virus 1
Mutation(s): No

Deposited: 2009-06-29 Released: 2011-04-27
Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.239
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Hydrogen bonds at the protein-inhibitor interface in the HIV-1 protease / inhibitors complexes probed by total chemical synthesis and X-ray crystallography

Torbeev, V.Y., Kent, S.B.H.

To be published.

Macromolecule Content

Total Structure Weight: 22.29 kDa
Atom Count: 1,784
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A, B	99	N/A	Mutation(s): 0 EC: 3.4.23.16
UniProt
Find proteins for O38732 (Human immunodeficiency virus 1) Explore O38732 Go to UniProtKB: O38732
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O38732
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2NC Query on 2NC Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide C₃₅ H₆₈ N₁₁ O₈ MQPXOVRKKPPKFZ-QYKDHROSSA-O		Interactions Focus chain C [auth B]

Modified Residues 4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	A, B	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
IIL Query on IIL	A, B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		ILE
NLE Query on NLE	A, B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU
YCM Query on YCM	A, B	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃ S		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000398 (2NC) Query on PRD_000398	C [auth B]	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide	Peptide-like / Inhibitor		Interactions Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.239
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.139	α = 90
b = 58.084	β = 90
c = 61.525	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2014-02-12
Changes: Refinement description

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.