3LIY | pdb_00003liy

crystal structure of HTLV protease complexed with Statine-containing peptide inhibitor

PDB DOI: https://doi.org/10.2210/pdb3LIY/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human T-cell leukemia virus type I
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-01-25 Released: 2010-07-14
Deposition Author(s): Satoh, T., Li, M., Nguyen, J., Kiso, Y., Wlodawer, A., Gustchina, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.222 (Depositor), 0.227 (DCC)
R-Value Work:
0.188 (Depositor), 0.193 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease.

Satoh, T., Li, M., Nguyen, J.T., Kiso, Y., Gustchina, A., Wlodawer, A.

(2010) J Mol Biology 401: 626-641

PubMed: 20600105 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jmb.2010.06.052
Primary Citation Related Structures:
3LIN, 3LIQ, 3LIT, 3LIV, 3LIX, 3LIY

PubMed Abstract:
Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailed study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.

Organizational Affiliation

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA.

Macromolecule Content

Total Structure Weight: 78.9 kDa
Atom Count: 5,970
Modeled Residue Count: 721
Deposited Residue Count: 726
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A B D [auth C] E [auth D] G [auth E] A, B, D [auth C], E [auth D], G [auth E], H [auth F]	116	Human T-cell leukemia virus type I	Mutation(s): 1 Gene Names: prt
UniProt
Find proteins for Q82134 (Human T-cell leukemia virus type I) Explore Q82134 Go to UniProtKB: Q82134
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82134
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
statine-containing inhibitor	C [auth I], F [auth J], I [auth K]	10	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain L [auth E] SDF format, chain J [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth E] MOL2 format, chain J [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth E] mmCIF format, chain J [auth A]	J [auth A], K [auth C], L [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth E]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000429 Query on PRD_000429	C [auth I], F [auth J], I [auth K]	(ACE)APQV(STA)VMHP peptide Inhibitor	Peptide-like / Inhibitor		Interactions Focus chain C [auth I] Focus chain F [auth J] Focus chain I [auth K] Interactions & Density Focus chain C [auth I] Focus chain F [auth J] Focus chain I [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.222 (Depositor), 0.227 (DCC)
R-Value Work: 0.188 (Depositor), 0.193 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.69	α = 90
b = 77.395	β = 99.69
c = 80.166	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2021-10-13
Changes: Database references, Derived calculations
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description
Version 1.6: 2023-11-22
Changes: Data collection
Version 1.7: 2024-11-27
Changes: Structure summary