9CH4 | pdb_00009ch4

Deposited: 2024-07-01 Released: 2026-03-18
Deposition Author(s): Castro, C.D., Adams, E.J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig-like domain-containing protein	A, C, E	268	Ginglymostoma cirratum	Mutation(s): 0 Gene Names: scyTo_0002318

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D, F	94	Ginglymostoma cirratum	Mutation(s): 0 Gene Names: B2M, b2m
UniProt
Find proteins for F4ZE04 (Ginglymostoma cirratum) Explore F4ZE04 Go to UniProtKB: F4ZE04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F4ZE04
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, J	6		N-Glycosylation	Interactions Focus chain G Focus chain J Interactions & Density Focus chain G Focus chain J
Glycosylation Resources
GlyTouCan: G88303DD GlyCosmos: G88303DD GlyGen: G88303DD

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	2		N/A	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
03F (Subject of Investigation/LOI) Query on 03F Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain R [auth C] SDF format, chain O [auth A] MOL2 format, chain S [auth E] MOL2 format, chain R [auth C] MOL2 format, chain O [auth A] mmCIF format, chain S [auth E] mmCIF format, chain R [auth C] mmCIF format, chain O [auth A]	O [auth A], R [auth C], S [auth E]	(9Z)-N-[(2S,3R,4E)-1-(beta-D-glucopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]octadec-9-enamide C₄₂ H₇₉ N O₈ MVGFIPNJBNBHNC-HVFXMTMESA-N		Interactions Focus chain O [auth A] Focus chain R [auth C] Focus chain S [auth E] Interactions & Density Focus chain O [auth A] Focus chain R [auth C] Focus chain S [auth E]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth A]	N [auth A], P [auth B], Q [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth C] Interactions & Density Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth C]