2XQY

CRYSTAL STRUCTURE OF PSEUDORABIES CORE FRAGMENT OF GLYCOPROTEIN H IN COMPLEX WITH FAB D6.3

PDB DOI: https://doi.org/10.2210/pdb2XQY/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Suid alphaherpesvirus 1, Mus musculus
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2010-09-08 Released: 2010-12-22
Deposition Author(s): Backovic, M., Dubois, R., Cockburn, J., Sharff, A., Vaney, M., Granzow, H., Klupp, B., Bricogne, G., Mettenleiter, T., Rey, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.205
R-Value Work: 0.188
R-Value Observed: 0.189

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: 227.88 kDa
Atom Count: 14,739
Modelled Residue Count: 1,796
Deposited Residue Count: 2,106
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE GLYCOPROTEIN H	A, B [auth E]	572	Suid alphaherpesvirus 1	Mutation(s): 0
UniProt
Find proteins for P27416 (Suid herpesvirus 1 (strain Kaplan)) Explore P27416 Go to UniProtKB: P27416
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27416
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A13-D6.3 MONOCLONAL ANTIBODY	C [auth G], D [auth J]	261	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
A13-D6.3 MONOCLONAL ANTIBODY	E [auth K], F [auth L]	220	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth B], H [auth C], I [auth D], J [auth F], K [auth H]	2		N-Glycosylation	Interactions Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth F] Focus chain K [auth H] Interactions & Density Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth F] Focus chain K [auth H]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 L [auth E] MOL2 format, chain L [auth E]	L [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth E] Interactions & Density Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.205
R-Value Work: 0.188
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.31	α = 90
b = 100.63	β = 94.02
c = 161.83	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-22
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary