5UV3 | pdb_00005uv3

Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor

PDB DOI: https://doi.org/10.2210/pdb5UV3/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human gammaherpesvirus 8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-17 Released: 2017-03-29
Deposition Author(s): Acker, T.M., Gable, J., Bohn, M.-F., Craik, C.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.237 (Depositor), 0.240 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (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

Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor

Acker, T.M., Craik, C.S., Bohn, M.-F.

To be published.

Macromolecule Content

Total Structure Weight: 43.93 kDa
Atom Count: 3,165
Modeled Residue Count: 380
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF 17	A, B	193	Human gammaherpesvirus 8	Mutation(s): 0 Gene Names: ORF17
UniProt
Find proteins for O40922 (Human herpesvirus 8) Explore O40922 Go to UniProtKB: O40922
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O40922
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8N4 Query on 8N4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-{[3-(trifluoromethoxy)phenyl]amino}benzoic acid C₂₇ H₂₆ F₃ N₃ O₄ OQQHKPTYNRWLGC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.237 (Depositor), 0.240 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.326	α = 90
b = 95.828	β = 90
c = 118.997	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling
PHENIX	phasing
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2023-10-04
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.