6W6Q | pdb_00006w6q

WT HTLV-1 Protease in Complex with Darunavir (DRV)

PDB DOI: https://doi.org/10.2210/pdb6W6Q/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human T-cell leukemia virus type I
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-17 Released: 2021-03-17
Deposition Author(s): Lockbaum, G.J., Henes, M., Kosovrasti, K., Nalivaika, E.A., Ali, A., KurtYilmaz, N., Schiffer, C.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.264 (Depositor), 0.260 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

To Be Determined

Lockbaum, G.J., Henes, M., Kosovrasti, K., Nalivaika, E.A., Ali, A., KurtYilmaz, N., Schiffer, C.A.

To be published.

Macromolecule Content

Total Structure Weight: 25.68 kDa
Atom Count: 1,813
Modelled Residue Count: 232
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTLV-1 Protease	A [auth B], B [auth A]	116	Human T-cell leukemia virus type I	Mutation(s): 0 Gene Names: pro
UniProt
Find proteins for P10274 (Human T-cell leukemia virus 1 (strain Japan ATK-1 subtype A)) Explore P10274 Go to UniProtKB: P10274
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
017 (Subject of Investigation/LOI) Query on 017 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]	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C₂₇ H₃₇ N₃ O₇ S CJBJHOAVZSMMDJ-HEXNFIEUSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.264 (Depositor), 0.260 (DCC)
R-Value Work: 0.229 (Depositor), 0.230 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.499	α = 90
b = 78.499	β = 90
c = 160.56	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Nalivaika, E.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01-GM109767

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, 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.