8Y9V | pdb_00008y9v

ZIKV NS2B/NS3 protease

PDB DOI: https://doi.org/10.2210/pdb8Y9V/pdb

Classification: HYDROLASE
Organism(s): Zika virus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-02-07 Released: 2024-02-28
Deposition Author(s): Zhang, C.Y., Xu, Q., Wang, W.W., Zhou, H., Wang, Q.S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.248 (Depositor), 0.247 (DCC)
R-Value Work:
0.217 (Depositor), 0.217 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8Y9V

This is version 1.0 of the entry. See complete history.

Literature

Crystallographic data collection using a multilayer monochromator on an undulator beamline at SSRF

Zhang, C.Y., Xu, Q., Liang, M., Yu, L., Li, M.J., Zhu, Z.M., Huang, L.Q., Li, Q.H., Yu, F., Wang, Y.Z., Zhou, H., Wang, Q.S.

To be published.

Macromolecule Content

Total Structure Weight: 45.95 kDa
Atom Count: 3,067
Modeled Residue Count: 387
Deposited Residue Count: 424
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A, C	53	Zika virus	Mutation(s): 0
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	B	153	Zika 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)
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	D	161	Zika 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)
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DAR-LYS-ORN-ARG	E	4	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAR Query on DAR	E	D-PEPTIDE LINKING	C₆ H₁₅ N₄ O₂		--
ORN Query on ORN	E	L-PEPTIDE LINKING	C₅ H₁₂ N₂ O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.248 (Depositor), 0.247 (DCC)
R-Value Work: 0.217 (Depositor), 0.217 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.753	α = 90
b = 59.753	β = 90
c = 213.594	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	21ZR1471800

Revision History (Full details and data files)

Version 1.0: 2024-02-28
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.