3NW8

Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH

PDB DOI: https://doi.org/10.2210/pdb3NW8/pdb

Classification: VIRAL PROTEIN
Organism(s): Human alphaherpesvirus 1 strain KOS
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2010-07-09 Released: 2010-12-01
Deposition Author(s): Stampfer, S.D., Lou, H., Cohen, G.H., Eisenberg, R.J., Heldwein, E.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.242
R-Value Work: 0.202
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 319.82 kDa
Atom Count: 19,958
Modelled Residue Count: 2,427
Deposited Residue Count: 2,812
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein B	A [auth B], B [auth A], C, D	703	Human alphaherpesvirus 1 strain KOS	Mutation(s): 1 Gene Names: gB, UL27 Membrane Entity: Yes
UniProt
Find proteins for P06437 (Human herpesvirus 1 (strain KOS)) Explore P06437 Go to UniProtKB: P06437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06437
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain K [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth A] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	CA [auth D] DA [auth D] G [auth B] H [auth B] K [auth B] CA [auth D], DA [auth D], G [auth B], H [auth B], K [auth B], M [auth A], N [auth A], O [auth A], S [auth A], X [auth C], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth A] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth A] Focus chain X [auth C] Focus chain Y [auth C]
MRY Query on MRY Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain U [auth A] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth C]	EA [auth D] I [auth B] J [auth B] P [auth A] Q [auth A] EA [auth D], I [auth B], J [auth B], P [auth A], Q [auth A], R [auth A], U [auth A], V [auth C], W [auth C], Z [auth C]	MESO-ERYTHRITOL C₄ H₁₀ O₄ UNXHWFMMPAWVPI-ZXZARUISSA-N		Interactions Focus chain EA [auth D] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A]	T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain FA [auth D] SDF format, chain L [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain L [auth B]	AA [auth C], BA [auth C], FA [auth D], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain L [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.242
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.985	α = 90
b = 117.985	β = 90
c = 321.537	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary