8QLN

Crystal structure of an N-terminal fragment of HCMV UL47

PDB DOI: https://doi.org/10.2210/pdb8QLN/pdb

Classification: VIRAL PROTEIN
Organism(s): Human herpesvirus 5 strain AD169
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2023-09-20 Released: 2024-10-02
Deposition Author(s): Rehfeld, C.L., Reubold, T.F., Eschenburg, S.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.251
R-Value Work: 0.214
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of an N-terminal fragment of HCMV UL47

Rehfeld, C.L., Reubold, T.F., Eschenburg, S.

To be published.

Macromolecule Content

Total Structure Weight: 63.8 kDa
Atom Count: 3,870
Modelled Residue Count: 466
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner tegument protein	A	546	Human herpesvirus 5 strain AD169	Mutation(s): 7 Gene Names: UL47
UniProt
Find proteins for P16784 (Human cytomegalovirus (strain AD169)) Explore P16784 Go to UniProtKB: P16784
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TEW Query on TEW Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	6-tungstotellurate(VI) O₂₄ Te W₆ JDLYBIMRCSJRQJ-UHFFFAOYSA-M		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.251
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.96	α = 90
b = 64.96	β = 90
c = 265.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	EXC 2155 RESIST Project ID 390874280

Revision History (Full details and data files)

Version 1.0: 2024-10-02
Type: Initial release

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.