6XDS

Crystal structure of MBP-TREM2 Ig domain fusion with fragment, 2-((4-bromophenyl)amino)ethan-1-ol

• PDB DOI: https://doi.org/10.2210/pdb6XDS/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Methanosarcina mazei, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-11 Released: 2021-02-17 
• Deposition Author(s): Su, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.208 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.13 kDa 
• Atom Count: 4,464 
• Modelled Residue Count: 485 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter substrate-binding protein,Triggering receptor expressed on myeloid cells 2	A	492	Methanosarcina mazei, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: malE, DU74_04045, TREM2
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q9NZC2 (Homo sapiens) Explore Q9NZC2  Go to UniProtKB:  Q9NZC2
PHAROS:  Q9NZC2 GTEx:  ENSG00000095970
UniProt Groups	Q9NZC2P0AEX9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G96370VA GlyCosmos:  G96370VA GlyGen:  G96370VA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V5S (Subject of Investigation/LOI)	C [auth A]	2-[(4-bromophenyl)amino]ethan-1-ol C8 H10 Br N O GYWMAZOWKOVMKS-UHFFFAOYSA-N
DMS	D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009	B	alpha-maltotriose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.208 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.84	α = 90
b = 80.35	β = 90
c = 103.89	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Su, H.P.

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release