6Y6C
TREM2 extracellular domain (19-174) in complex with single-chain variable fragment (scFv-4)
- PDB DOI: https://doi.org/10.2210/pdb6Y6C/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens, Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2020-02-26 Released: 2021-02-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.26 Å
- R-Value Free: 0.216 
- R-Value Work: 0.191 
- R-Value Observed: 0.192 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Triggering receptor expressed on myeloid cells 2 | 202 | Homo sapiens | Mutation(s): 0  Gene Names: TREM2 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9NZC2 (Homo sapiens) Explore Q9NZC2  Go to UniProtKB:  Q9NZC2 | |||||
PHAROS:  Q9NZC2 GTEx:  ENSG00000095970  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9NZC2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Single chain variable | 245 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth A], 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: 2.26 Å
- R-Value Free: 0.216 
- R-Value Work: 0.191 
- R-Value Observed: 0.192 
- Space Group: P 41 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 111.661 | α = 90 |
b = 111.661 | β = 90 |
c = 232.196 | γ = 90 |
Software Name | Purpose |
---|---|
PHASER | phasing |
PHENIX | refinement |
PHENIX | data processing |
Coot | model building |
xia2 | data processing |
xia2 | data reduction |
DIALS | data scaling |
Entry History 
Deposition Data
- Released Date: 2021-02-17  Deposition Author(s): Szykowska, A., Preger, C., Williams, E., Mukhopadhyay, S.M.M., McKinley, G., Gruslund, S., Wigren, E., Persson, H., Arrowsmith, C.H., Edwards, A., von Delft, F., Bountra, C., Davis, J.B., Di Daniel, E., Burgess-Brown, N., Bullock, A.
Revision History (Full details and data files)
- Version 1.0: 2021-02-17
Type: Initial release - Version 1.1: 2021-07-21
Changes: Database references - Version 1.2: 2021-11-17
Changes: Data collection, Database references - Version 1.3: 2022-12-21
Changes: Data collection, Database references, Source and taxonomy - Version 1.4: 2024-01-31
Changes: Data collection, Refinement description