5UR3 | pdb_00005ur3

Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor

PDB DOI: https://doi.org/10.2210/pdb5UR3/pdb

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

Deposited: 2017-02-09 Released: 2017-03-08
Deposition Author(s): Acker, T.M., Gable, J., Bohn, M.-F., Craik, C.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.221 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 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: 43.67 kDa
Atom Count: 3,320
Modeled Residue Count: 382
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KSHV protease	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O40922
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8OY Query on 8OY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	C [auth A], D [auth B], E [auth B]	4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-(phenylamino)benzoic acid C₂₆ H₂₇ N₃ O₃ PIPBPJWDZSBLMQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.221 (DCC)
R-Value Work: 0.180 (Depositor), 0.182 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.4	α = 90
b = 92.86	β = 90
c = 118.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH R01 GM104659
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1F32GM111012

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2024-03-06
Changes: Data collection, Database references

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