9DD8 | pdb_00009dd8

Deposited: 2024-08-27 Released: 2025-09-10
Deposition Author(s): Roark, R.S., Shapiro, L., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

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

Literature

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein B	A, D [auth B], G [auth C]	808	Human alphaherpesvirus 1	Mutation(s): 1 Gene Names: UL27, HHV1gp041
UniProt
Find proteins for A1Z0P7 (Human herpesvirus 1) Explore A1Z0P7 Go to UniProtKB: A1Z0P7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1Z0P7
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain D [auth B] Focus chain G [auth C]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D48 heavy chain	B [auth H], E [auth I], H [auth J]	238	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
D48 light chain	C [auth L], F [auth M], I [auth N]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth D], L [auth F], N [auth K]	7		N-Glycosylation	Interactions Focus chain J [auth D] Focus chain L [auth F] Focus chain N [auth K] Interactions & Density Focus chain J [auth D] Focus chain L [auth F] Focus chain N [auth K]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth E], M [auth G], O	2		N-Glycosylation	Interactions Focus chain K [auth E] Focus chain M [auth G] Focus chain O Interactions & Density Focus chain K [auth E] Focus chain M [auth G] Focus chain O
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 U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A]	P [auth A] Q [auth A] R [auth B] S [auth B] T [auth C] P [auth A], Q [auth A], R [auth B], S [auth B], T [auth C], U [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth C]