Research workbench
TREM2 extracellular domain (19-174) in complex with single-chain variable fragment (scfv-4)
Analyse TREM2 extracellular domain (19-174) 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
- 6Y6C
- Type
- protein
- Length
- 693 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triggering receptor expressed on myeloid cells 2; Single chain variable
- UniProt
- Q9NZC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triggering receptor expressed on myeloid cells 2 | protein | 118 | 5% helix, 53% strand | Q9NZC2 |
| C | Single chain variable | protein | 228 | 5% helix, 50% strand | — |
| D | Single chain variable | protein | 229 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.43 | 0.75 | 21 | NAG |
| 2 | 139 | 0.42 | 0.75 | 29 | empty |
| 3 | 117 | 0.39 | 0.75 | 24 | empty |
| 4 | 109 | 0.37 | 0.75 | 28 | empty |
| 5 | 79 | 0.36 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 898 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 886 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 453 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 450 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 431 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y6C · TREM2 extracellular domain (19-174) 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 0.95
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 6Y6C · PDBe 6Y6C · UniProt Q9NZC2
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