3IA9 | pdb_00003ia9

Crystal structure of a chemically synthesized [D25N]HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor

PDB DOI: https://doi.org/10.2210/pdb3IA9/pdb

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

Deposited: 2009-07-13 Released: 2011-07-27
Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.208 (Depositor), 0.215 (DCC)
R-Value Work:
0.178 (Depositor), 0.187 (DCC)
R-Value Observed:
0.179 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 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: 22.48 kDa
Atom Count: 1,794
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
[D25N]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 2 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 A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	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 A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

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_000398 (2NC) Query on PRD_000398	C [auth A]	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 A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.208 (Depositor), 0.215 (DCC)
R-Value Work: 0.178 (Depositor), 0.187 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.09	α = 90
b = 57.697	β = 90
c = 61.832	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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-07-27
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary

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