3DCK | pdb_00003dck

X-ray structure of D25N chemical analogue of HIV-1 protease complexed with ketomethylene isostere inhibitor

PDB DOI: https://doi.org/10.2210/pdb3DCK/pdb

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

Deposited: 2008-06-03 Released: 2008-08-19
Deposition Author(s): Torbeev, V.Y., Mandal, K., Terechko, V.A., Kent, S.B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.224 (DCC)
R-Value Work:
0.194 (Depositor), 0.195 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site

Torbeev, V.Y., Mandal, K., Terechko, V.A., Kent, S.B.H.

(2008) Bioorg Med Chem Lett 18: 4554-4557

PubMed: 18657969 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.07.039
Primary Citation Related Structures:
3DCK, 3DCR

PubMed Abstract:
Here we report the X-ray structures of chemically synthesized HIV-1 protease and the inactive [D25N]HIV-1 protease complexed with the ketomethylene isostere inhibitor Ac-Thr-Ile-Nle psi[CO-CH(2)]Nle-Gln-Arg.amide at 1.4 and 1.8A resolution, respectively. In complex with the active enzyme, the keto-group was found to be converted into the hydrated gem-diol, while the structure of the complex with the inactive D25N enzyme revealed an intact keto-group. These data support the general acid-general base mechanism for HIV-1 protease catalysis.

Organizational Affiliation

Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA. torbeev@uchicago.edu

Macromolecule Content

Total Structure Weight: 22.3 kDa
Atom Count: 1,656
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemical analogue HIV-1 protease	A, B	99	N/A	Mutation(s): 0 EC: 3.4.23.16
UniProt
Find proteins for O38732 (Human immunodeficiency virus type 1) Explore O38732 Go to UniProtKB: O38732
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O38732
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KVI Query on KVI 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]	(2S)-2-{[(2R,5S)-5-{[(2S,3S)-2-{[(2S,3R)-2-(acetylamino)-3-hydroxybutanoyl]amino}-3-methylpentanoyl]amino}-2-butyl-4-oxononanoyl]amino}-N~1~-[(2S)-1-amino-5-carbamimidamido-1-oxopentan-2-yl]pentanediamide C₃₆ H₆₆ N₁₀ O₉ ARYLRJRVHGPIHO-XPRREXDTSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	A, B	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
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_001174 (KVI) Query on PRD_001174	C [auth B]	(2S)-2-{[(2R,5S)-5-{[(2S,3S)-2-{[(2S,3R)-2-(ACETYLAMINO)-3-HYDROXYBUTANOYL]AMINO}-3-METHYLPENTANOYL]AMINO}-2-BUTYL-4-OXONONANOYL]AMINO}-N~1~-[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]PENTANEDIAMIDE	Peptide-like / Inhibitor		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.224 (DCC)
R-Value Work: 0.194 (Depositor), 0.195 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.028	α = 90
b = 58.551	β = 90
c = 61.584	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-08-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-08-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2013-10-16
Changes: Non-polymer description
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-03-20
Changes: Source and taxonomy, Structure summary