4MYV

Free HSV-2 gD structure

PDB DOI: https://doi.org/10.2210/pdb4MYV/pdb

Classification: VIRAL PROTEIN
Organism(s): Human herpesvirus 2 strain 333
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2013-09-28 Released: 2014-10-01
Deposition Author(s): Lu, G., Zhang, N., Qi, J., Li, Y., Chen, Z., Zheng, C., Yan, J., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.230
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 66.43 kDa
Atom Count: 3,240
Modelled Residue Count: 352
Deposited Residue Count: 588
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 D	A, B	294	Human herpesvirus 2 strain 333	Mutation(s): 0 Gene Names: gD, US6
UniProt
Find proteins for P03172 (Human herpesvirus 2 (strain 333)) Explore P03172 Go to UniProtKB: P03172
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03172
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.230
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.562	α = 90
b = 55.351	β = 96.35
c = 65.335	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-01
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2022-08-24
Changes: Database references, Structure summary
Version 1.3: 2023-11-08
Changes: Data collection, Refinement description

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Help and Resources

4MYV

Free HSV-2 gD structure

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)