3SLZ | pdb_00003slz

The crystal structure of XMRV protease complexed with TL-3

PDB DOI: https://doi.org/10.2210/pdb3SLZ/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): DG-75 Murine leukemia virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-06-27 Released: 2011-10-12
Deposition Author(s): Li, M., Gustchina, A., Wlodawer, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.201 (Depositor)
R-Value Work:
0.176 (Depositor)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and biochemical characterization of the inhibitor complexes of xenotropic murine leukemia virus-related virus protease.

Li, M., Gustchina, A., Matuz, K., Tozser, J., Namwong, S., Goldfarb, N.E., Dunn, B.M., Wlodawer, A.

(2011) FEBS J 278: 4413-4424

PubMed: 21951660 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1111/j.1742-4658.2011.08364.x
Primary Citation Related Structures:
3SLZ, 3SM1, 3SM2

PubMed Abstract:
Interactions between the protease (PR) encoded by the xenotropic murine leukemia virus-related virus and a number of potential inhibitors have been investigated by biochemical and structural techniques. It was observed that several inhibitors used clinically against HIV PR exhibit nanomolar or even subnanomolar values of K(i) , depending on the exact experimental conditions. Both TL-3, a universal inhibitor of retroviral PRs, and some inhibitors originally shown to inhibit plasmepsins were also quite potent, whereas inhibition by pepstatin A was considerably weaker. Crystal structures of the complexes of xenotropic murine leukemia virus-related virus PR with TL-3, amprenavir and pepstatin A were solved at high resolution and compared with the structures of complexes of these inhibitors with other retropepsins. Whereas TL-3 and amprenavir bound in a predictable manner, spanning the substrate-binding site of the enzyme, two molecules of pepstatin A bound simultaneously in an unprecedented manner, leaving the catalytic water molecule in place.

Organizational Affiliation

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA.

Macromolecule Content

Total Structure Weight: 29.9 kDa
Atom Count: 2,166
Modeled Residue Count: 228
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gag-pro-pol polyprotein	A, B	132	DG-75 Murine leukemia virus	Mutation(s): 0 Gene Names: gag-pol
UniProt
Find proteins for Q9E7M1 (DG-75 Murine leukemia virus) Explore Q9E7M1 Go to UniProtKB: Q9E7M1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9E7M1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3TL Query on 3TL 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]	benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate C₅₀ H₆₄ N₆ O₁₀ BJJPNOGMLLUCER-KUTQPOQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A] E [auth A] F [auth B] G [auth B] H [auth B] D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000434 (3TL) Query on PRD_000434	C [auth A]	N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide	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: 1.40 Å
R-Value Free: 0.201 (Depositor)
R-Value Work: 0.176 (Depositor)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.483	α = 90
b = 65.546	β = 90
c = 69.732	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Li, M.

Gustchina, A.

Wlodawer, A.

Revision History (Full details and data files)

Version 1.0: 2011-10-12
Type: Initial release
Version 1.1: 2012-04-04
Changes: Database references
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations