5XEQ

Crystal Structure of human MDGA1 and human neuroligin-2 complex

• PDB DOI: https://doi.org/10.2210/pdb5XEQ/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-04-05 Released: 2017-07-12 
• Deposition Author(s): Kim, H.M., Kim, J.A., Kim, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.278 
• R-Value Work: 0.234 
• R-Value Observed: 0.238 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 100.23 kDa 
• Atom Count: 6,450 
• Modelled Residue Count: 817 
• Deposited Residue Count: 895 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroligin-2	A	576	Homo sapiens	Mutation(s): 1  Gene Names: NLGN2, KIAA1366
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFZ4 (Homo sapiens) Explore Q8NFZ4  Go to UniProtKB:  Q8NFZ4
PHAROS:  Q8NFZ4 GTEx:  ENSG00000169992

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAM domain-containing glycosylphosphatidylinositol anchor protein 1	B	319	Homo sapiens	Mutation(s): 0  Gene Names: MDGA1, MAMDC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFP4 (Homo sapiens) Explore Q8NFP4  Go to UniProtKB:  Q8NFP4
PHAROS:  Q8NFP4 GTEx:  ENSG00000112139

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth B], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.278 
• R-Value Work: 0.234 
• R-Value Observed: 0.238 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.875	α = 90
b = 69.134	β = 115.31
c = 108.843	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Kim, H.M., Kim, J.A., Kim, D.

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary