2FP7 | pdb_00002fp7

West Nile Virus NS2B/NS3protease in complex with Bz-Nle-Lys-Arg-Arg-H

PDB DOI: https://doi.org/10.2210/pdb2FP7/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): West Nile virus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-01-16 Released: 2006-03-07
Deposition Author(s): Schiering, N., D'Arcy, A., Erbel, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.219 (Depositor), 0.289 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus.

Erbel, P., Schiering, N., D'Arcy, A., Renatus, M., Kroemer, M., Lim, S.P., Yin, Z., Keller, T.H., Vasudevan, S.G., Hommel, U.

(2006) Nat Struct Mol Biol 13: 372-373

PubMed: 16532006 Search on PubMed
DOI: https://doi.org/10.1038/nsmb1073
Primary Citation Related Structures:
2FOM, 2FP7

PubMed Abstract:
The replication of flaviviruses requires the correct processing of their polyprotein by the viral NS3 protease (NS3pro). Essential for the activation of NS3pro is a 47-residue region of NS2B. Here we report the crystal structures of a dengue NS2B-NS3pro complex and a West Nile virus NS2B-NS3pro complex with a substrate-based inhibitor. These structures identify key residues for NS3pro substrate recognition and clarify the mechanism of NS3pro activation.

Organizational Affiliation

Novartis Institutes for Biomedical Research, Protease Platform, 4002 Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 25.35 kDa
Atom Count: 1,619
Modeled Residue Count: 192
Deposited Residue Count: 231
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	54	West Nile virus	Mutation(s): 0 EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P06935 (West Nile virus) Explore P06935 Go to UniProtKB: P06935
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06935
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B	172	West Nile virus	Mutation(s): 0 EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P06935 (West Nile virus) Explore P06935 Go to UniProtKB: P06935
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06935
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-benzoyl-L-norleucyl-L-lysyl-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-argininamide	C	5	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE Query on NLE	C	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU
OAR Query on OAR	C	PEPTIDE-LIKE	C₆ H₁₆ N₄ O		ARG

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000988 Query on PRD_000988	C	N-benzoyl-L-norleucyl-6-ammonio-L-norleucyl-N~5~-[amino(iminio)methyl]-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-ornithinamide	Peptide-like / Inhibitor		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.219 (Depositor), 0.289 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.182 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.425	α = 90
b = 93.425	β = 90
c = 47.435	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
CNX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-03-07

Deposition Author(s):

Schiering, N.

D'Arcy, A.

Erbel, P.

Revision History (Full details and data files)

Version 1.0: 2006-03-07
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2011-11-02
Changes: Structure summary
Version 1.4: 2013-02-27
Changes: Other
Version 1.5: 2017-06-28
Changes: Database references, Source and taxonomy, Structure summary
Version 1.6: 2017-10-18
Changes: Refinement description
Version 1.7: 2018-02-14
Changes: Experimental preparation
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-04-03
Changes: Refinement description