Research workbench
TREM2 extracellular domain (19-131) in complex with single-chain variable fragment (scfv-2)
Analyse TREM2 extracellular domain (19-131) in complex with single-chain variable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YYE
- Type
- protein
- Length
- 684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triggering receptor expressed on myeloid cells 2; TREM2 single chain variable 2
- UniProt
- Q9NZC2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triggering receptor expressed on myeloid cells 2 | protein | 112 | 6% helix, 55% strand | Q9NZC2 |
| B | Triggering receptor expressed on myeloid cells 2 | protein | 109 | 3% helix, 54% strand | Q9NZC2 |
| C | TREM2 single chain variable 2 | protein | 231 | 3% helix, 46% strand | — |
| D | TREM2 single chain variable 2 | protein | 232 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.71 | 0.76 | 87 | empty |
| 2 | 50 | 0.39 | 0.82 | 19 | empty |
| 3 | 133 | 0.39 | 0.74 | 27 | empty |
| 4 | 58 | 0.38 | 0.80 | 17 | empty |
| 5 | 77 | 0.38 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 712 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 651 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 639 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6YYE · TREM2 extracellular domain (19-131) in complex with single-chain variable fragment… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZC2 · AlphaFold monomer V2.0 prediction for triggering receptor expressed on myeloid cells 2… · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9NZC2
- Elsewhere: RCSB PDB 6YYE · PDBe 6YYE · UniProt Q9NZC2
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