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Crystal structure of the human myeloid cell activating receptor trem-1

Analyse Crystal structure of the human myeloid cell activating receptor trem-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Q8M
Type: protein
Length: 484 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Triggering receptor expressed on myeloid cells 1
UniProt: Q9NP99
Ligands: GSH, SO4
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Triggering receptor expressed on myeloid cells 1	protein	121	5% helix, 53% strand	Q9NP99

Ligands and binding sites

GSH · Glutathione · ligand · chains A, B
SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.67	0.97	17	empty

Interfaces

3 interfaces between chains.

C–D · 2178 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2041 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 545 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1Q8M · Crystal structure of the human myeloid cell activating receptor TREM-1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9NP99 · AlphaFold monomer V2.0 prediction for triggering receptor expressed on myeloid cells 1… · a predicted model of the same protein · chain A against A, TM-score 0.88

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 Q9NP99
Elsewhere: RCSB PDB 1Q8M · PDBe 1Q8M · UniProt Q9NP99

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