5HXF | pdb_00005hxf

Crystal structure of 3C protease from a mild Human enterovirus 71 in complex with rupintrivir

PDB DOI: https://doi.org/10.2210/pdb5HXF/pdb

Classification: HYDROLASE
Organism(s): Enterovirus A71
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-01-30 Released: 2017-02-15
Deposition Author(s): Li, B., Yuan, Z., Qin, L., Gu, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.199 (Depositor), 0.202 (DCC)
R-Value Work:
0.174 (Depositor), 0.179 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of 3C protease from a mild Human enterovirus 71 in complex with rupintrivir

Li, B., Yue, Y., Zhang, Y., Yuan, Z., Liu, Y., Li, P., Song, N., Li, Z., Gu, L., Qin, L.

To be published.

Macromolecule Content

Total Structure Weight: 21.09 kDa
Atom Count: 1,761
Modeled Residue Count: 182
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C protease	A	184	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for B8YLW0 (Human enterovirus 71) Explore B8YLW0 Go to UniProtKB: B8YLW0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YLW0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AG7 Query on AG7 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER C₃₁ H₄₁ F N₄ O₇ LMIUALQNZXJHOG-IFILWLFVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.199 (Depositor), 0.202 (DCC)
R-Value Work: 0.174 (Depositor), 0.179 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.209	α = 90
b = 64.781	β = 113.06
c = 38.323	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-02-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-02-15
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.