4KGG

Deposited: 2013-04-29 Released: 2013-08-07
Deposition Author(s): Liu, W., Bonanno, J.B., Zhan, C., Kumar, P.R., Toro, R., Nathenson, S.G., Almo, S.C., Atoms-to-Animals: The Immune Function Network (IFN), New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 6B	A [auth C], B [auth D]	174	Homo sapiens	Mutation(s): 0 Gene Names: TNFRSF6B, DCR3, TR6, UNQ186/PRO212
UniProt & NIH Common Fund Data Resources
Find proteins for O95407 (Homo sapiens) Explore O95407 Go to UniProtKB: O95407
PHAROS: O95407 GTEx: ENSG00000243509
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95407
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 14	C [auth A], D [auth B]	158	Homo sapiens	Mutation(s): 4 Gene Names: TNFSF14, HVEML, LIGHT, UNQ391/PRO726
UniProt & NIH Common Fund Data Resources
Find proteins for O43557 (Homo sapiens) Explore O43557 Go to UniProtKB: O43557
PHAROS: O43557 GTEx: ENSG00000125735
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43557
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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	F	2		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Unit Cell:

Software Package:

Entry History

Deposition Author(s):

Liu, W.

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2013-09-18
Changes: Structure summary
Version 1.2: 2014-12-31
Changes: Database references
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: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary