5X5W | pdb_00005x5w

Crystal structure of pseudorabies virus glycoprotein D

PDB DOI: https://doi.org/10.2210/pdb5X5W/pdb

Classification: VIRAL PROTEIN/CELL ADHESION
Organism(s): Suid alphaherpesvirus 1, Sus scrofa
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2017-02-17 Released: 2017-04-26
Deposition Author(s): Li, A., Lu, G., Qi, J., Wu, L., Tian, K., Luo, T., Shi, Y., Yan, J., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.266 (Depositor), 0.266 (DCC)
R-Value Work:
0.238 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of pseudorabies virus glycoprotein D

Li, A., Lu, G., Qi, J., Wu, L., Tian, K., Luo, T., Shi, Y., Yan, J., Gao, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 112.97 kDa
Atom Count: 5,542
Modeled Residue Count: 680
Deposited Residue Count: 1,018
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GD	A, C	402	Suid alphaherpesvirus 1	Mutation(s): 0 Gene Names: US6
UniProt
Find proteins for P07645 (Suid herpesvirus 1 (strain Rice)) Explore P07645 Go to UniProtKB: P07645
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07645
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nectin-1	B, D	107	Sus scrofa	Mutation(s): 0 Gene Names: NECTIN1, HVEC, PRR1, PVRL1
UniProt
Find proteins for Q9GL76 (Sus scrofa) Explore Q9GL76 Go to UniProtKB: Q9GL76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GL76
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.266 (Depositor), 0.266 (DCC)
R-Value Work: 0.238 (Depositor), 0.240 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.945	α = 90
b = 98.11	β = 90
c = 128.395	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-04-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-26
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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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.